Culture

BU researchers use amazon reviews and AI to predict product recalls

An AI named BERT identified recalled foods from Amazon customer reviews with 74-percent accuracy, then found thousands of potentially unsafe but unrecalled products.

The Food and Drug Administration (FDA) can take months to identify and verify a problem before issuing a product recall, so most recalls come from manufacturers, often after enough people have gotten sick to generate bad press. But soon, artificial intelligence could comb through online reviews to identify serious threats to public health, and speed the process of a product recall, according to a new study co-authored by a Boston University School of Public Health (BUSPH) researcher.

In the study, published in the Journal of the American Medical Informatics Association (JAMIA) Open, the researchers taught an existing "deep-learning" AI called Bidirectional Encoder Representation from Transformations (BERT) to predict food product recalls from Amazon reviews with about 74-percent accuracy. The AI also identified 20,000 reviews that suggested potentially unsafe food products that had not been investigated.

"Health departments in the US are already using data from Twitter, Yelp, and Google for monitoring foodborne illnesses," says the study's senior author, Dr. Elaine Nsoesie, assistant professor of global health at BUSPH. She explains that, in contrast, this study was able to look at the safety of specific food products. "Tools like ours can be effectively used by health departments or food product companies to identify consumer reviews of potentially unsafe products, and then use this information to decide whether further investigation is warranted."

BERT is trained on large bodies of English-language text, including English Wikipedia, and can interpret text for a given purpose. Nsoesie and her colleagues used crowdsourcing (by real humans) to categorize 6,000 of the reviews that contained words related to FDA recall reasons, such as "sick," "label," "ill," "foul," "rotten," etc., along with metadata such as the review's title and star rating. BERT was able to look at these same customer reviews and correctly identify recalled food products with 74-percent accuracy. It then found terms associated with FDA recalls in 20,000 other reviews.

Credit: 
Boston University School of Medicine

UTA study: Urban sprawl creates food deserts

image: Shima Hamidi, director of UTA's Center for Transportation Equity, Decisions and Dollars, published "Urban sprawl and the emergence of food deserts in the USA" in Urban Studies Journal.

Image: 
UT Arlington

Urban sprawl has led to the creation of food deserts in metropolitan areas across the United States, according to a published study by a researcher at The University of Texas at Arlington.

Shima Hamidi, director of UTA's Center for Transportation Equity, Decisions and Dollars, published "Urban sprawl and the emergence of food deserts in the USA" in Urban Studies Journal.

"We believe the analysis is one of the first national attempts to account for urban sprawl and other built-environment and socioeconomic characteristics of a neighborhood," Hamidi said. "This study found that, in addition to socioeconomic characteristics, urban sprawl at both neighborhood and regional levels increases the likelihood of a neighborhood becoming or having a food desert.

"More compact neighborhoods are likely to support a greater number of grocery stores and have healthy food stores in close proximity."

The U.S. Department of Agriculture defines a food desert as a low-income area where a significant number of residents live more than one mile in urban areas or more than 10 miles in rural areas from a supermarket, big-box supercenter or other healthy grocery store. About 20% of residents in Dallas and Tarrant counties live in food deserts with no access to healthy food options.

Hamidi said the study reveals that increasing the housing density increases the chances of a neighborhood landing stores that provide good, healthy food. More compact regions reduce racial and income segregation, thus allowing for a greater opportunity of stores offering healthy food to enter the community.

Her research shows that while financial incentives might prove effective in the short term, more systematic, longer-range solutions--such as increasing housing density, making communities more walkable and allowing a diversity of land uses--are far more beneficial to a neighborhood in luring a supermarket.

Duane Dimos, UTA vice president for research, said Hamidi's study reflects UTA's focus on Sustainable Urban Communities, one of the themes of the University's Strategic Plan 2020.

"Urban sprawl is not unique to Dallas--it exists throughout the nation," Dimos said. "Many U.S. metropolitan areas suffer from the maladies associated with it. We have an opportunity through Dr. Hamidi's research to combat urban sprawl with techniques that translate to many, many metropolitan areas. Being smarter and thinking outside the box will serve us well in building and rebuilding America's urban areas."

In another published study, Hamidi linked urban sprawl to decreased life expectancy. And in The Costs of Sprawl, a book she wrote in 2017, Hamidi shows how sprawl affects health and other quality-of-life outcomes.

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University of Texas at Arlington

Deciphering pancreatic cancer's invade and evade tactics

Two known gene mutations induce pathways that enhance pancreatic cancer's ability to invade tissues and evade the immune system. Researchers report the molecular details of this process providing insights into druggable targets for immunotherapies.

Mutations in the genes KRAS and TP53 are closely linked to pancreatic ductal adenocarcinoma, by far the most common type of pancreatic cancer. Pancreatic cancers are often already malignant when diagnosed, making its five-year survival rate extremely low -- less than ten percent. So, understanding how it evolves at the molecular level could help anti-cancer drug development.

Hisataka Sabe of Hokkaido University and colleagues in Japan conducted tests in human cancer cells and in mouse models of the disease to investigate the roles of KRAS and TP53 gene mutations in pancreatic ductal adenocarcinoma. The study was published in the journal Proceedings of the National Academy of Sciences (PNAS).

They found that mutations in KRAS increased the production of two proteins, called ARF6 and AMAP1, which they previously discovered constitute a signalling pathway involved in cancer cell invasion and malignancy.

Mutations in the gene TP53 were also found to facilitate ARF6 activation, in addition to causing a metabolic pathway, called the mevalonate pathway, to go into overdrive. This pathway is known for its role in enhancing the invasiveness of some cancers.

Further investigations of the ARF6-AMAP1 pathway found it was involved in promoting cell-surface expression of an immune checkpoint protein, called PD-L1, on cancer cells, in addition to enhancing its recycling within the cell. PD-L1 expression on cancer cells helps them hide from the immune system, avoiding attack. Mutated KRAS and TP53 genes, and over-activation of the mevalonate pathway, both played crucial roles in the eventual cell-surface expression and recycling of PD-L1.

"We found that two well-known driver mutations of pancreatic cancer can promote both invasion to other tissues and evasion of the immune system through promoting the ARF6 pathway. This means that malignancies can develop in parallel with oncogenesis, making it difficult to detect cancer cells in its early stage," says Hisataka Sabe. "Further studies are still needed to determine the extent of PD-L1 involvement in immune evasion. Studies are also needed to consider if PD-L1- and ARF6-targeting drugs can make pancreatic cancer cells more susceptible to attack by the immune system," he continued.

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Hokkaido University

New study: Ocean temperature 'surprises' becoming more common

image: Around the world, periods of rapid ocean warming are happening more often than we thought. In order to thrive in the future, marine communities need to make decisions based on climate trends rather than historical data.

Image: 
Gulf of Maine Research Institute

PORTLAND, Maine -- August 5, 2019 -- A new study published this week shows how marine ecosystems around the world are experiencing unusually high ocean temperatures more frequently than researchers previously expected. These warming events, including marine heatwaves, are disrupting marine ecosystems and the people who depend on them.

Dr. Andrew Pershing, Chief Scientific Officer at the Gulf of Maine Research Institute, led the study, which is entitled "Challenges to natural and human communities from surprising ocean temperatures," and published in the Proceedings of the National Academy of Sciences (PNAS).

As part of this new research effort, Dr. Pershing, whose research previously identified the Gulf of Maine as one of the most rapidly warming ecosystems in the global ocean, looked at similar warming trends around the globe.

Dr. Pershing and his colleagues examined 65 large marine ecosystems from 1854-2018 to identify the frequency of surprising ocean temperatures, which they defined as an annual mean temperature that is two standard deviations above the mean of the previous three decades.

The researchers identified these "surprises" all over the world, including the Arctic, North Atlantic, eastern Pacific, and off of Australia. Moreover, these warming events occurred at nearly double the rate the scientists expected.

"Across the 65 ecosystems we examined, we expected about six or seven of them would experience these 'surprises' each year," explains Pershing. "Instead, we've seen an average of 12 ecosystems experiencing these warming events each year over the past seven years, including a high of 23 'surprises' in 2016."

The study explores the associated impacts of these warming events on both natural and human communities.

In natural communities (e.g. coral reefs, fish, plankton, etc.), new species that prefer warmer conditions can often replace cold-loving species that suffer when an ecosystem warms. In gradually warming ecosystems, the changeover of species should be able to keep pace, according to the study. However, in ecosystems that are experiencing change much faster, these natural communities are expected to suffer reductions in both biomass and diversity.

An increase in ocean "surprises" also affects humans. The researchers explored the challenge rapid ecosystem changes pose to people making decisions about ocean resources. As the planet continues to warm, ecosystems and human communities will adapt to the changing conditions. However, according to the scientists, it is unclear whether such adjustments will keep pace as the climate trends accelerate.

As part of the study, the research team compared two distinct community decision-making strategies. Using an economic model, they compared forward-looking decisions based on climate trends to the results of decisions made only on historical experiences. They found forward looking decisions fare much better as the rate of warming increases.

According to the study, many marine ecosystems are already warming fast enough to apply this decision-making framework.

"We are entering a world where history is an unreliable guide for decision making," says Pershing. "In a rapidly changing world, betting that trends will continue is a much better strategy."

As the incidence of these extreme warming events continues to rise, the results of this study highlight the importance of using climate projections and other predictive tools to make decisions about the future.

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Gulf of Maine Research Institute

Targeting DNA sequencing for plant biodiversity research

Third-generation sequencing (TGS) technologies like the portable MinION sequencer promise to revolutionize biology, but getting there will require tweaking techniques. Particularly, the low output delivered by TGS sequencers means that targeted sequencing approaches will have to be developed to assure proper sequencing coverage of regions of interest. In research presented in a recent issue of Applications in Plant Sciences, Dr. Thomas Couvreur and colleagues developed a new protocol to capture and sequence longer segments of plastome DNA in plants.

"New sequencing technologies like the MinION can play a pivotal role in accelerating biodiversity discovery and understanding its functioning and evolution, especially in the tropics. This is because sequencing is becoming more portable and easy to do," said Dr. Couvreur, corresponding author on the article and Director of Research at the French National Institute for Research for Sustainable Development (IRD) in Montpellier, France. "We were thus interested in improving our lab protocols to better integrate these technologies for biodiversity research."

In particular, Dr. Couvreur and colleagues were interested in capturing and sequencing long fragments of chloroplast DNA using a technique called targeted sequencing, which had never been used for long DNA fragments in plants. They designed probes to capture these long sequences and tested the protocol in six monocots--three grasses and three palms. Dr. Couvreur describes the targeted capture as "a bit like fishing. We basically hook the DNA we are interested in and then sequence it."

Targeted sequencing combined with TGS technology could improve genome assembly, or the computational stitching together of many sequenced DNA fragments into larger continuous blocks. The short reads produced by older sequencing technologies, typically 100-400 base pairs long, make bioinformatic assembly of certain genomic regions like repetitive sequences very difficult. Third-generation sequencing technologies such as the portable MinION produce longer reads that could help produce these assemblies. However, these sequencers generally have lower data output than older sequencing technologies. Therefore, to efficiently sequence regions of interest, these regions must be enriched through methods like targeted capture and sequencing.

"Longer fragments makes assembling genomes easier. One can compare this to a puzzle with 1000 small pieces (short reads) versus 10 large pieces," explained Dr. Couvreur. "Our research question was simple: can we capture long DNA fragments for targeted sequencing?" The team did succeed in capturing long fragments of plastome DNA. The median fragment length was 3151 base pairs long on average across trials, much longer than the ~400 base pair fragments delivered by older sequencing technologies.

"This method can be used to assemble plastomes, or at least significantly improve assembly," said Dr. Couvreur. "Our protocol will be particularly useful for non-model plant species, for which we have little or no prior data on the plastome." This can help in phylogenetic and other analyses of non-model plants, which represent the vast majority of plant biodiversity.

"The field of targeted sequencing is changing quickly, and improved protocols will no doubt enhance plastome assembly," concluded Dr. Couvreur. "For now, we show that capturing and subsequently sequencing long DNA fragments is possible, which is a first step."

Credit: 
Botanical Society of America

Brain reorganization predicts language production

image: These are MRI scans of the lesions in each stroke patient.

Image: 
François et al., <i>eNeuro</i> 2019

The right hemisphere of the brain can take over language functions when the left hemisphere is damaged early in development, according to research in four-year-old children published in eNeuro. These findings offer insight into typical language development in children and the flexibility of the brain in response to injury.

Language functions are typically localized in the left hemisphere of the brain, a distinction that is present at birth but becomes more pronounced during development. Damage to the language regions of the left hemisphere often causes speech aphasia, which does not generally happen in child stroke patients.

In order to study the flexibility of language development, Clément François and colleagues at the University of Barcelona compared the brains and language skills of healthy children with children that had a left-hemisphere stroke as infants. Using magnetic resonance imaging, the research team observed that the arcuate fasciculus, a white-matter fiber bundle that connects language-processing brain regions, had a greater volume in the right hemisphere and a lower volume in the left hemisphere in the stroke patients. Among the stroke patients, the children with the largest right volume performed best on language tests.

Credit: 
Society for Neuroscience

How deep space travel could affect the brain

image: Radiation exposure alters the electrophysiological properties of neurons in the hippocampus.

Image: 
Acharya et al., <em>eNeuro</em> 2019

Exposure to chronic, low dose radiation -- the conditions present in deep space -- causes neural and behavioral impairments in mice, researchers report in eNeuro. These results highlight the pressing need to develop safety measures to protect the brain from radiation during deep space missions as astronauts prepare to travel to Mars.

Radiation is known to disrupt signaling among other processes in the brain. However, previous experiments used short-term, higher dose-rate exposures of radiation, which does not accurately reflect the conditions in space.

To investigate how deep space travel could affect the nervous system, Charles Limoli and colleagues at the University of California, Irvine, Stanford University, Colorado State University and the Eastern Virginia School of Medicine exposed mice to chronic, low dose radiation for six months. They found that the radiation exposure impaired cellular signaling in the hippocampus and prefrontal cortex, resulting in learning and memory impairments. They also observed increased anxiety behaviors, indicating that the radiation also impacted the amygdala.

The researchers predict that during a deep space mission approximately one in five astronauts would experience anxiety-like behavior and one in three would experience certain levels of memory impairments. Additionally, the astronauts may struggle with decision-making.

Credit: 
Society for Neuroscience

Link between intimate partner homicide and firearms dealters in urban settings

CAMDEN - Much attention continues to be given to crimes committed with illegal guns, but there are high risks of intimate partner homicide with legally purchased firearms as well, according to a new Rutgers University-Camden study.

The pioneering study - conducted by Richard Stansfield and Daniel Semenza, assistant professors of criminal justice at Rutgers-Camden - shows a significant link between the concentration of federally licensed firearms dealers in urban counties and intimate partner homicide in the home.

"This study showed this robust association regardless of whether the victims were male or female or how old the victims were," says Stansfield.

The forthcoming study, to be published in the September 2019 issue of the journal Preventive Medicine, is the first to investigate the connection between firearms dealers and intimate partner homicide at the county level, and one of only a handful ever to examine how access to legal guns through federally licensed firearm dealers in the community is linked to gun violence.

The Rutgers-Camden researchers - affiliated scholars of the Rutgers Center for Gun Violence Research - note that they did not find the same association between federally licensed firearms dealers and intimate partner homicide in rural counties. They posit that, in rural areas, people are more likely to own a gun in the home and thus are less reliant on going out to a gun store to purchase one after an argument with the intent of harming or killing an intimate partner. However, in urban areas, where fewer people own guns in the home, having more licensed firearms dealers takes on added significance.

"If there is greater access to legal guns, it could make it easier for someone to purchase a gun in the throes of an argument, before there is time to cool off," explains Semenza. "We can't definitively say that's the dynamic here, but this study backs prior research indicating that this greater access shows an increased risk."

Furthermore, the Rutgers-Camden researchers explain, prior studies show that, when intimate partner violence occurs, more than likely firearms are used in the commission of the crime.

"This underscores the importance of examining where guns are coming from," says Stansfield.

Semenza says that, from a policy perspective, they would like to see their research inform gun laws that make it more difficult for perpetrators of intimate partner violence to have easy access to guns, especially those with a history of domestic violence.

The Rutgers-Camden researchers also hope that this study is the first of many research projects focusing on the connection between access to legal guns and various types of violence.

"We are trying to draw out the why, what, and how local gun stores matter," says Stansfield.

However, he says, one of the biggest barriers to their research is the limited data available on how guns purchased legally at gun stores get into the hands of perpetrators of intimate partner violence. They hope to access complete police reports showing this data.

"Until then, we can't make any determinations that the person making the purchase is the one using the gun," says Semenza, who notes that they use the Centers for Disease Control and Prevention definition of an intimate partner as a current or former partner or spouse and does not require sexual intimacy.

Stansfield adds that they also plan to study how this link between legal gun access and different crimes varies according to population density and racial demographics, as well as determine what types of gun stores are more implicated - whether it is the larger, big-box retailers or smaller, local stores that have more established relationships in an area.

Furthermore, they note, the best place to analyze these associations - "to look at the nitty gritty of this research," says Semenza - is to track the proximity of these stores to incidents rather than the higher-level estimates at the county and state levels.

"It might require looking at it from a spatial mapping perspective in order to take this study further than what we are looking at today," says Semenza.

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Rutgers University

Gender bending: Baby turtles influence their own sex

Baby turtles influence their gender by moving around inside their eggs, research has revealed.

The idea that an embryo reptile can act in a way that affects its chances of developing as male or female has long been thought impossible, but findings by scientists from China and Australia have now provided clear proof of the process.

The research, published in the journal Current Biology, solves a long-standing evolutionary mystery - and offers hope that at least some species thought especially vulnerable to effects of climate change will prove more robust than thought.

To carry out their work the scientists, led by Wei-Guo Du from the Chinese Academy of Science in Beijing and including Macquarie University biologist Rick Shine, incubated several clutches of eggs laid in semi-natural nests by a species of freshwater turtle, Mauremys reevesii.

Like those of many other reptiles, the eggs of the turtle are crucially dependent on the temperature of the nest. It has long been known that warmth influences gender in such species - a condition known as temperature-dependent sex determination, or TSD.

The prevalence of TSD has raised fears for the survival of many reptile species as global warming bites. When temperatures rise, scientists suggest, the usual 50-50 gender ratio will be heavily skewed, reducing reproduction rates to unsustainable levels.

Not all the evidence, however, leads to the same conclusion - a fact that led Du, Shine and colleagues to investigate.

"Reconstruction of the ancestral lineages of many TSD species shows that they have survived for millions of years," says Shine, "including during periods where the average temperatures were much hotter than current climate change models predict."

Although maternal behaviours such as changing egg-laying times and altering nest structures to avoid the hottest times of the year might explain part of this stubborn survival, adult reptiles are powerless to protect their developing young from temperature changes once the eggs have been laid.

To find out, thus, whether turtle embryos were influence their own genders the researchers manipulated conditions affecting M. reevseii eggs.

They found that when warmed by a heat source set at an angle each egg developed a significant thermal gradient, becoming warmer at one end. The embryos then moved inside the eggs in response. Those that shifted toward the warmer end developed into females, while those heading into the cold became male.

The researchers suspected that the embryos were detecting the temperatures through inbuilt bio-sensors called ion channels. To test this, they administered a drug which blocked ion activity, but did not otherwise affect the health of the animals.

They found that the treated embryos did not move as far as untreated ones, and that sex ratios quickly became skewed. In cold conditions, almost all the turtles turned out male, with females dominating at higher temperatures.

"The discovery that embryos can influence their own development is truly remarkable," says Shine.

He adds that the findings constitute a rare "good news" story about conservation.

"Turtles are in desperate trouble all over the world - for example they are eaten in Asia, and their habitats are being destroyed by short-sighted management of river systems in Australia," he explains.

"It's encouraging to know that turtles may be better than we expected at dealing with some of the challenges wrought by climate change."

For co-author Wei-Guo Du, the research provided a vindication of earlier work. A previous study by his team suggesting that movements by turtle embryos were triggered by temperature zones within eggs received a sceptical reception by some other scientists in the field. The new findings reinforce his initial conclusions.

"We previously demonstrated that reptile embryos could move around within their egg for thermoregulation, so we were curious about whether this could affect their sex determination," he says.

"We wanted to know if and how this behaviour could help buffer the impact of global warming on offspring sex ratios in these species."

Six of the seven scientists collaborating in the study are based in China - a fact, says Shine, that demonstrates the strength of the research community in that country.

"Ecological and evolutionary research is flourishing in China, backed by substantial government investment and driven by a new generation of young Chinese scholars," he says.

"Increasingly, some of the best research about critical issues like climate change is coming from China."

Credit: 
Macquarie University

SUTD researchers develop a rapid, low-cost method to 3D print microfluidic devices

image: Concept and demonstrations of microfluidic devices fabricated using DIW 3D printer. Demonstrated devices includes: Mixer, cell culture chamber, droplet generator, multilayer gradient generator, flow resistor, integrated electrodes and integrated porous membranes.

Image: 
SUTD

Microfluidics is the manipulation and study of sub-microscopic liters of fluids. Technologies that utilise microfluidics are found in many multidisciplinary fields ranging from engineering to biology. Experiments can be performed on a device roughly of the size of a dollar coin, reducing the amount of reagents used, wastes produced, and the overall costs. Experiments can be conducted precisely at microscale levels, offering reduced reaction times and improved control over the reaction conditions.

Current gold standard for the fabrication of microfluidic devices is soft lithography, where elastomeric materials are casted on a mold fabricated in a cleanroom. Despite multiple desirable characteristics to fabricate microfluidic channels, however, soft lithography is a manual process that is difficult to automate. Typically, soft lithography has a design-to-prototype cycle of a few days.

3D printing emerged as an attractive alternative to soft lithography. Not only can 3D printers turn design into actual working prototypes in the order of hours, recent introduction of low-cost 3D printers make 3D printing more accessible in general to researchers. Current 3D printing technologies for the fabrication of microfluidic devices have a few limitations, namely;

available materials for 3D printing (e.g. optical transparency, flexibility, biocompatibility),

achievable dimensions of microchannels by commercial 3D printers,

integration of 3D printed microfluidics with functional materials or substrates.

To overcome these challenges, researchers from the Singapore University of Technology and Design's (SUTD) Soft Fluidics Lab have developed an alternative method to apply 3D printing for the fabrication of microchannels. The researchers applied direct ink writing (DIW) 3D printing of fast-curing silicone sealant to fabricate microfluidic devices rapidly on various substrates (e.g. glass, plastic, and membranes). The design of fluidic channels is determined by the patterned silicone sealant, while the top and bottom transparent substrates serve to seal the channels. The use of transparent substrates allows the researchers to image the channel using a microscope. This method also permits the fabrication of microfluidic channels that are dynamically tunable in dimensions, which served as small channels as well as tunable flow resistors.

"By controlling the distance between the top and bottom substrates, we were able to precisely reduce the channel width up to around 30 microns. This lateral dimension of the channels would be difficult to obtain if commercially available 3D printers were employed," said lead author Terry Ching, a graduate student from SUTD's Engineering Product Development pillar.

"Our approach to apply DIW 3D printing allows direct patterning of microchannels essentially on any flat substrate" said Assistant Professor Michinao Hashimoto, the principal investigator of the project.

The team also demonstrated the ease of patterning of silicone barriers directly on an off-the-shelf printed circuit board (PCB), immediately integrating electrodes into the microchannels that would function as real-time flow sensors. Rapid integration of semi-permeable membranes to microchannels for culturing Keratinocyte cells was demonstrated.

Credit: 
Singapore University of Technology and Design

Using quantum dots and a smartphone to find killer bacteria

image: This is a diagram depicting the analysis process.

Image: 
Sunna Lab

A combination of off-the-shelf quantum dot nanotechnology and a smartphone camera soon could allow doctors to identify antibiotic-resistant bacteria in just 40 minutes, potentially saving patient lives.

Staphylococcus aureus (golden staph), is a common form of bacterium that causes serious and sometimes fatal conditions such as pneumonia and heart valve infections. Of particular concern is a strain that does not respond to methicillin, the antibiotic of first resort, and is known as methicillin-resistant S. aureus, or MRSA.

Recent reports estimate that 700 000 deaths globally could be attributed to antimicrobial resistance, such as methicillin-resistance. Rapid identification of MRSA is essential for effective treatment, but current methods make it a challenging process, even within well-equipped hospitals.

Soon, however, that may change, using nothing except existing technology.

Researchers from Macquarie University and the University of New South Wales, both in Australia, have demonstrated a proof-of-concept device that uses bacterial DNA to identify the presence of Staphylococcus aureus positively in a patient sample - and to determine if it will respond to frontline antibiotics.

In a paper published in the international peer-reviewed journal Sensors and Actuators B: Chemical the Macquarie University team of Dr Vinoth Kumar Rajendran, Professor Peter Bergquist and Associate Professor Anwar Sunna with Dr Padmavathy Bakthavathsalam (UNSW) reveal a new way to confirm the presence of the bacterium, using a mobile phone and some ultra-tiny semiconductor particles known as quantum dots.

"Our team is using Synthetic Biology and NanoBiotechnology to address biomedical challenges. Rapid and simple ways of identifying the cause of infections and starting appropriate treatments are critical for treating patients effectively," says Associate Professor Anwar Sunna, head of the Sunna Lab at Macquarie University.

"This is true in routine clinical situations, but also in the emerging field of personalised medicine."

The researchers' approach identifies the specific strain of golden staph by using a method called convective polymerase chain reaction (or cPCR). This is a derivative of a widely -employed technique in which a small segment of DNA is copied thousands of times, creating multiple samples suitable for testing.

Vinoth Kumar and colleagues then subject the DNA copies to a process known as lateral flow immunoassay - a paper-based diagnostic tool used to confirm the presence or absence of a target biomarker. The researchers use probes fitted with quantum dots to detect two unique genes, that confirms the presence of methicillin resistance in golden staph

A chemical added at the PCR stage to the DNA tested makes the sample fluoresce when the genes are detected by the quantum dots - a reaction that can be captured easily using the camera on a mobile phone.

The result is a simple and rapid method of detecting the presence of the bacterium, while simultaneously ruling first-line treatment in or out.

Although currently at proof-of-concept stage, the researchers say their system which is powered by a simple battery is suitable for rapid detection in different settings.

"We can see this being used easily not only in hospitals, but also in GP clinics and at patient bedsides," says lead author, Macquarie's Vinoth Kumar Rajendran.

Credit: 
Macquarie University

TV crews capture first evidence of leopard seals sharing food

image: Up to 36 seals were seen feeding at the same king penguin colony in South Georgia.

Image: 
James Robbins/University of Plymouth

Drone footage has shown never-before seen behaviour of two leopard seals sharing food.

Despite being considered a charismatic and enigmatic Antarctic predator, leopard seals are normally thought of as being solitary.

They are largely intolerant of each other but can be forced to hunt alongside one another when congregating in areas of abundant prey.

A new study analysing the previously unseen footage reports up to 36 seals seen feeding at the same king penguin colony in South Georgia.

It also highlights examples of two seals feeding on the same penguin carcass, the first evidence of such behaviour ever being recorded.

However, scientists add it is unclear if it is a case of true cooperation, or whether both seals were simply accepting the competitor so that they didn't have to chase them away, potentially leading to them losing their prey completely.

Published in Polar Biology, the study was led by James Robbins, a Visiting Research Fellow at the University of Plymouth and formerly with the British Antarctic Survey.

He said: "Leopard seals are often portrayed as the villains - chasing fluffy penguins in Happy Feet and creating havoc in the Antarctic. In reality, little is known about these enigmatic creatures, and these observations provide key insights into their behaviour and social antics.

"The footage has given us an exciting new insight into the behaviour and lives of leopard seals. There is still so much that we don't understand about these predators as they live in remote areas of the Antarctic and are often seen alone on an inaccessible iceberg. But I've personally had over 500 encounters with leopard seals and have never seen two animals being so tolerant of each other."

This isn't the first time that a documentary has allowed previously unknown behaviours to be captured on film. Past media expeditions have recorded killer whales creating waves to wash seals off icebergs, and leopard seals appearing to feed human divers.

In the latter case, it was assumed to be a rare case of gift-giving, but the authors of this study now suggest that cooperative feeding may be a more likely explanation.

They suggest it is more energetically expensive to defend a large kill than it is to tolerate kleptoparasitism (the stealing of food), and that rather than chasing away competitors, seals focus on each gaining some of the food without using large amounts of energy.

David Hocking from Monash University, another author on the paper, added: "The remoteness of Antarctic ecosystems can make it challenging to connect with the wildlife there, but this new footage provides a rare window into that world. Early Antarctic explorers described leopard seals as the 'principle enemy of the penguin', but most observations show seals targeting smaller penguin species. This study shows that even large adult king penguins are at risk when leopard seals are around.

"This study also provides a great example of how new technology is helping researchers to make close-hand observations of wild animals. By using a camera drone, the filmmakers were able to fly above the animals without disturbing them, revealing detailed behaviours that otherwise may have gone unnoticed to shore-based observers."

Editor's Note: This release has been updated since it was originally published by request of the submitting institution. Sentences referring to the Netflix series have been removed.

Credit: 
University of Plymouth

Researchers create first-ever 'map' of global labor flow

image: The study revealed large-scale associations between industries and people across the globe. Each circle represents a specific geo-industrial cluster with its size proportional to its number of employees.

Image: 
Image by Jaehyuk Park, Indiana University

A small team of researchers at Indiana University has created the first global map of labor flow in collaboration with the world's largest professional social network, LinkedIn. The work is reported in the journal Nature Communications.

The study's lead authors are Jaehyuk Park and Ian Wood, Ph.D. students working with Yong Yeol "Y.Y." Ahn, a professor at the IU School of Informatics, Computing and Engineering in Bloomington.

According to the researchers, the study's result represents a powerful tool for understanding the flow of people between industries and regions in the U.S. and beyond. It could also help policymakers better understand how to address critical skill gaps in the labor market or connect workers with new opportunities in nearby communities.

The study showed some unexpected connections between economic sectors, such as the strong ties between credit card and airline industries. It also identified growing industries during the study period from 2010 to 2014, including the pharmaceutical and oil and gas industries -- with in-demand skills such as team management and project management -- as well as declining industries, such as retail and telecommunications.

IU researchers created the map using LinkedIn's data on 500 million people between 1990 and 2015, including about 130 million job transitions between more than 4 million companies. The researchers gained access to this rare data as one of only 11 teams selected to participate in the inaugural LinkedIn Economic Graph Research program in 2015. They later became one of only two teams -- IU and MIT -- selected to continue their work beyond 2017. The team worked closely with LinkedIn engineers, including Michael Conover, a graduate of the IU School of Informatics, Computing and Engineering and a senior data scientist at LinkedIn at the time of the study.

In a blog post on LinkedIn, Park compares the study to a "roadmap" to the future economy since the first step in any journey requires understanding the current landscape.

"We expect this study will provide a powerful foundation for further systematic analysis of geo-industrial clusters in the context of business strategy, urban economics, regional economics and international development fields -- as well as providing useful insights for policymakers and business leaders," he said.

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Indiana University

How 'natural-killer' cells might help women avoid a deadly risk of childbirth

image: These microscopic slides of mouse placentas and uterine tissue show the importance of the protein Gab3 for ensuring a healthy delivery. On the left, in normal, wild-type mice (WT) the brown-colored cells, the placental trophoblast, form an area called the junctional zone (JZ) and few cells enter vessels in the maternal decidua (DB). The uterine wall and the rest of the decidua (DB) are clear. This allows the placenta to detach properly during delivery. The middle image shows much deeper penetration when mice have a mutated form of Gab3. The image on the right shows even deeper penetration when mice completely lack Gab3. The last two conditions result in retained placenta, a high risk of severe bleeding and possible death for the mother. Detailed findings were posted online Aug. 2 in Science Immunology.

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Cincinnati Children's

One of the most dangerous risks expectant mothers face as their delivery date approaches is a surprisingly common condition with a little-known name: placental accreta.

In normal childbirth, the placenta that sustains fetal development during pregnancy is delivered shortly after the newborn infant. But sometimes, the placenta becomes so deeply attached to the woman's uterus that it cannot be removed without causing massive, sometimes fatal bleeding. In many cases, the emergency surgery needed to save the mother's life can leave her unable to have any more children.

And yet, many people do not know about placental accreta, even though the number of women diagnosed with it has quadrupled since the 1980s to one in every 272 births. While this increase is associated with a rise in c-section rate, the link remains unclear.

"I had never heard the word accreta until it happened to me, and I barely survived," says Kristen Terlizzi, who founded the California-based National Accreta Foundation in 2017. "A reliable biomarker to detect this would be incredible. And if there ever were a way to proactively treat accreta, that would be enormous."

That distant day may have moved a step closer thanks to a discovery made by scientists at Cincinnati Children's and the University of Cincinnati.

In a study published Aug. 2, 2019, in Science Immunology, co-authors describe a surprising connection between accreta risk and a gene mutation that prevents healthy formation of "natural killer" cells--a type of white blood cell that helps the body fight off cancer tumors and viral infections. Beyond discovering the connection, the team further demonstrated, in mice, that accreta can be stopped in its tracks.

"This is a huge issue for maternal health," says study co-author Helen Jones, PhD, an expert in placenta research at Cincinnati Children's. "Currently, the only way to diagnose accreta is to spot it mid-pregnancy on ultrasound, usually after 18 to 20 weeks. Many women never know they have it until they arrive at the hospital for labor and delivery."

If future studies confirm that women facing accreta also have malfunctioning NK cells, it may become possible to prevent over-attachment and reduce the need for fertility-ending hysterectomies, Jones says.

Accidental discovery connects accreta to malfunctioning NK cells

This new finding traces back to a basic-science project that had been led by Kasper Hoebe, PhD, a scientist with Cincinnati Children's Division of Immunobiology who recently left for a new position. His team was searching for gene mutations that can affect NK cells. During this work, Anna Sliz, a graduate student in Hoebe's lab, encountered a problem.

"In one of our colonies, we observed an abnormally high frequency of breeding dams having unsuccessful pregnancies. When I attempted to culture NK cells from these mice, I tended to have a lower yield compared to my wild-type controls," Sliz says.

Hoebe and Sliz consulted with Jones, who rapidly recognized that the dams were experiencing retained placentas with significant trophoblast invasion, reflective of human accreta--a condition rarely seen in mice. This prompted a new investigation.

Soon, the collaborators discovered that the mice carried a mutation in a protein called Gab3, which prevented normal NK cell expansion in the uterus. The disrupted NK cells then failed to do an important job: turning off the process that allows the growing embryo to attach to tissues inside the uterus.

This process, called trophoblast invasion, normally continues until about 20 weeks of pregnancy. But for women with accreta, the invasion process continues much longer.

"For normal placental development to occur, the growth of fetal cells must be held in check by NK cells," Hoebe says. "Our studies showed that in the absence of Gab3, NK cell function in the placenta is impaired, leading to an over-invasion of fetal cells into the uterus."

What does this mean for pregnant women?

Much more research must be done before women can be tested to determine if they have malfunctioning NK cells, and if an NK cell transplant would be safe and effective.

NK cells have been transplanted to treat people with certain forms of cancer, but the potential impacts on a pregnancy are not yet known.

"We don't know yet because we still need to investigate this in humans. We are working now on an international collaboration to try to work this out," Jones says.

For now, however, the findings may serve as a reminder to women to be cautious about receiving C-sections. Previous studies have shown that accreta risk rises sharply when women have multiple C-sections, and now these findings may contribute to explaining why that risk rises, Jones says.

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Cincinnati Children's Hospital Medical Center

Socially active 60-year-olds face lower dementia risk

Being more socially active in your 50s and 60s predicts a lower risk of developing dementia later on, finds a new UCL-led study.

The longitudinal study, published in PLOS Medicine, reports the most robust evidence to date that social contact earlier in life could play an important role in staving off dementia.

"Dementia is a major global health challenge, with one million people expected to have dementia in the UK by 2021, but we also know that one in three cases are potentially preventable," said the study's lead author, Dr Andrew Sommerlad (UCL Psychiatry).

"Here we've found that social contact, in middle age and late life, appears to lower the risk of dementia. This finding could feed into strategies to reduce everyone's risk of developing dementia, adding yet another reason to promote connected communities and find ways to reduce isolation and loneliness."

The research team used data from the Whitehall II study, tracking 10,228 participants who had been asked on six occasions between 1985 and 2013 about their frequency of social contact with friends and relatives. The same participants also completed cognitive testing from 1997 onwards, and researchers referred to the study subjects' electronic health records up until 2017 to see if they were ever diagnosed with dementia.

For the analysis, the research team focused on the relationships between social contact at age 50, 60 and 70, and subsequent incidence of dementia, and whether social contact was linked to cognitive decline, after accounting for other factors such as education, employment, marital status and socioeconomic status.

The researchers found that increased social contact at age 60 is associated with a significantly lower risk of developing dementia later in life. The analysis showed that someone who saw friends almost daily at age 60 was 12% less likely to develop dementia than someone who only saw one or two friends every few months.

They found similarly strong associations between social contact at ages 50 and 70 and subsequent dementia; while those associations did not reach statistical significance, the researchers say that social contact at any age may well have a similar impact on reducing dementia risk.

Social contact in mid to late life was similarly correlated with general cognitive measures.

Previous studies have found a link between social contact and dementia risk, but they did not have such long follow-up times, so they could not rule out the possibility that the beginnings of cognitive decline may have been causing people to see fewer people, rather than the other way around. The long follow-up in the present study strengthens the evidence that social engagement could protect people from dementia in the long run.

The researchers say there are a few explanations for how social contact could reduce dementia risk.

"People who are socially engaged are exercising cognitive skills such as memory and language, which may help them to develop cognitive reserve - while it may not stop their brains from changing, cognitive reserve could help people cope better with the effects of age and delay any symptoms of dementia," said senior author Professor Gill Livingston (UCL Psychiatry).

"Spending more time with friends could also be good for mental wellbeing, and may correlate with being physically active, both of which can also reduce the risk of developing dementia," added Professor Livingston, who previously led a major international study outlining the lifecourse factors that affect dementia risk.*

The researchers were supported by Wellcome and the National Institute for Health Research UCLH Biomedical Research Centre, while the Whitehall II study is supported by the US National Institutes of Health, UK Medical Research Council and the British Heart Foundation.

The study was conducted by researchers in UCL Psychiatry, UCL Epidemiology & Public Health, Camden & Islington NHS Foundation Trust and Inserm.

Dr Kalpa Kharicha, Head of Innovation, Policy and Research at the Campaign to End Loneliness, said: "We welcome these findings that show the benefits of frequent social contact in late/middle age on dementia risk. As we found in our Be More Us Campaign, almost half of UK adults say that their busy lives stop them from connecting with other people. It's important we make changes to our daily lives to ensure we take the time to connect with others. We need more awareness of the benefits that social wellbeing and connectedness can have to tackle social isolation, loneliness and reduce dementia risk."

Fiona Carragher, Chief Policy and Research Officer at Alzheimer's Society, said: "There are many factors to consider before we can confirm for definite whether social isolation is a risk factor or an early sign of the condition - but this study is a step in the right direction. We are proud of supporting work which helps us understand the condition better - it is only through research that we can understand true causes of dementia and how best to prevent it.

"As the number of people in the UK with dementia is set to rise to one million by 2021, we must do what we can to reduce our risk - so along with reducing your alcohol intake and stopping smoking, we encourage people across the country to get out into the sunshine, and do something active with family and friends.

"The Government's recent emphasis on health prevention is a welcome opportunity to reduce the risk of dementia across society. We now need to see Ministers prioritise better support initiatives to help people reduce the risk of dementia, and look forward to seeing this when the results of the Green Paper on Prevention are published later in the year."

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University College London