Earth

Warmer winters are changing the makeup of water in Black Sea

image: This graphic shows the positions of Argo floats, identified by the color in the right hand corner, that were sampling data from 2005 to 2018. The letters V, E, B, and S mark locations where a weather station collected surface data. Researchers compared those measurements with to the Black Sea's cold intermediate layer's warming trend.

Image: 
American Geophysical Union

WASHINGTON - Warmer winters are starting to alter the structure of the Black Sea, which could foreshadow how ocean compositions might shift from future climate change, according to new research.

A new study published in AGU's Journal of Geophysical Research: Oceans analyzing water temperatures, density and salinity in the Black Sea from 2005 to 2019 finds warming winter weather is warming the middle water layer of the Black Sea, known as the cold intermediate layer, which exists between the oxygen-free bottom layer of the sea and the oxygenated top layer of water. This warming is causing the cold intermediate layer to mix with the other two layers of water, according to the new research.

This intermediate layer has fluctuated in the past, but in the last 14 years its core temperature has warmed 0.7 degrees Celsius (1.26 degrees Fahrenheit). The blending of the cold intermediate layer with the other layers of water could enable the water masses from the deeper layers of the sea to eventually infiltrate the top layer, which would have unknown impacts on the sea's marine life.

The new study suggests climate change is causing the intermediate layer to warm and change, but natural fluctuations could also be playing a role, according to the study's authors.

Studying changes in smaller water bodies like the Black Sea shows scientists how larger bodies of water might evolve in the future. The new study suggests what might happen to Earth's oceans as the climate continues to warm, according to the researchers.

Water masses, which exist in bodies of water around the globe, influence Earth's climate and move nutrients around the world. Changes in oceanic masses' composition could reshape global currents, affecting the planet's climate and ecosystems.

It is difficult to study massive water masses in the oceans so scientists use regional water masses like those in the Black Sea to determine how climate change could be affecting oceanic masses.

"We want to at least know what could happen under different global climate change scenarios," said Emil Stanev, a physical oceanographer at Helmholtz-Zentrum Geesthacht Center for Materials and Coastal Research in Geesthacht, Germany, and lead author of the new study.

Changing water masses

The Black Sea lies between the Balkans and Eastern Europe and receives water from many major European rivers. It also receives and loses water through the Bosporus Strait, which links the Black Sea to the Mediterranean. The Black Sea's water stratification comes from the mixing of different water sources, creating water masses within the sea.

Water masses have distinct temperatures, salinities, and densities, usually identified by their horizontal and vertical positions in bodies of water. The Black Sea's cold intermediate water mass's depth varies depending on its distance from the shore. The mass separates low-saline surface water from the high-saline bottom water. Each of the sea's water layers hosts specific organisms suited to its oceanographic conditions.

Scientists previously studied the Black Sea's cold intermediate layer, but they had not analyzed how it has changed over time.

"They didn't pay too much attention to the evolution of the water masses," Stanev said.

In the new study, Stanev and his colleagues charted the evolution of the Black Sea's cold intermediate water mass for 14 years, comparing its progression with the region's climate trends. They used battery-powered floats to measure the temperature, density and salinity from the sea surface down to 1000 meters (3281 feet) at various points throughout the seasons. They then compared the float data to surface air temperatures to see if there was a correlation between warmer winters and changes in the cold intermediate water mass's temperature and salinity.

They found winter weather fluctuations changed the temperature and salinity of the cold intermediate layer, but the density of the water mass remained almost the same. The Black Sea's cold intermediate layer became warmer, allowing its edges to blend with the top and bottom layers of the sea. If this trend continues, it could potentially change the stratification of the sea, according to the study's authors. Restructuring the layers could bring sulfides, corrosive and noxious chemicals at the bottom of the sea, up to the surface, impacting marine wildlife and tourism.

Climate change might be warming the sea, but natural variability could also be responsible, according to James Murray, a chemical oceanographer at the University of Washington, who was not connected with the new study. Past research both by Murray and other scientists has shown the Black Sea's water layers have cycled through warm and cool periods since the 1950s.

However, the Black Sea's cold intermediate layer has never been this warm, Murray added.

Both Stanev and Murray agree that more research on the evolution of the Black Sea's layers is necessary. Continuing to study the Black Sea's cold intermediate layer and its fluctuations will indicate whether climate change is behind the layer's gradual disappearance.

Credit: 
American Geophysical Union

New tools help detect digital domestic abuse

ITHACA, N.Y. - A new clinical model developed by Cornell Tech researchers aims to respond systematically and effectively to the growing array of digital threats against victims of intimate partner violence. Working with the New York City Mayor's Office to End Domestic and Gender-Based Violence, the researchers created and piloted a questionnaire, a spyware scanning tool and a diagram for assessing clients' digital footprints.

The first-of-its-kind model can help counselors without tech expertise pinpoint online abuse - and protect the safety of abuse victims and their advisers. Using this strategy, researchers found potential spyware, compromised accounts or exploitable misconfigurations for 23 of the 44 clients they advised.

"Prior to this work, people were reporting that the abusers were very sophisticated hackers, and clients were receiving inconsistent advice," said Diana Freed, Cornell Tech doctoral student in the field of information science and co-lead author of "Clinical Computer Security for Victims of Intimate Partner Violence," presented Aug. 14 at the USENIX Security Symposium in Santa Clara, California.

"Some people were saying, 'Throw your device out.' Other people were saying, 'Delete the app.' But there wasn't a clear understanding of how this abuse was happening and why it was happening," Freed said. "We felt that a methodical approach through a uniform, data-driven consultation would yield better results so we can help other advocates do this type of work at the level it's needed."

Co-first author of the paper is Sam Havron, Cornell Tech doctoral student in computer science. Senior authors are Nicola Dell, assistant professor at the Jacobs Technion-Cornell Institute at Cornell Tech, and Thomas Ristenpart, associate professor at Cornell Tech.

The authors are among the researchers from Cornell Tech, Cornell in Ithaca and New York University collaborating to improve technological safety and security for survivors of intimate partner violence. Dell and Ristenpart were recently awarded a $1.2 million grant from the National Science Foundation to continue their research examining the role of tech in intimate partner abuse.

Abusers use a range of digital tools to stalk or harass their victims, from traditional spyware to tracking apps intended for more benign purposes, like finding one's phone. It can be extremely challenging to detect vulnerabilities amid the sheer number of apps, digital devices and online accounts most people use daily - particularly for counselors without tech skills.

"They were making their best efforts, but there was no uniform way to address this," Havron said. "They were using Google to try to help clients with their abuse situations."

At the same time, tech experts don't have the background to advise clients how to fix problems in ways that won't endanger them, such as angering an abuser who just noticed a deleted app or a changed password.

The researchers run a weekly tech clinic in New York City's Family Justice Centers, which provide a full range of services for intimate partner abuse victims. Through this work, the team developed and piloted its Technology Assessment Questionnaire, which includes such questions as, "Does the abuser show up unexpectedly or know things they shouldn't know?" and "Is there a chance the abuser knows (or could guess) the answers to your password reset questions?"

They also created the "technograph," a diagram which helps summarize clients' digital assets; and ISDi (IPV Spyware Discovery), a spyware scanning tool. ISDi scans devices for known spyware apps through a USB cable, rather than a downloadable app, making it impossible for an abuser to detect.

"This sort of tool doesn't exist anywhere else," Havron said. "In earlier work, we did a comprehensive scrape of the Google Play Store and eventually compiled a list of thousands of apps across marketplaces, and that's what the ISDi is based on."

The questionnaire, technograph and ISDi are all freely available on the project team's website.

Though the paper focused on intimate partner abuse, this method could be useful for any victims of online abuse, such as activists, dissidents or journalists, the researchers said.

"It's consistent, it's data-driven and it takes into account at each phase what the abuser will know if the client makes changes," Freed said. "This is giving people a more accurate way to make decisions and providing them with a comprehensive understanding of how things are happening."

Credit: 
Cornell University

Cardiovascular Innovations and Applications (CVIA) vol 4, issue 2 publishes

Beijing, 06 August 2019: the journal Cardiovascular Innovations and Applications (CVIA) has just published a new issue, Volume 4 Issue 2. This issue is a general issue with a wide variety of papers by authors from the US, Asia and Europe. This is also the first issue with new Editor in Chief Jianzeng Dong who will be working as joint Editor in Chief with C Richard Conti.

Papers in the issue are as follows:

REVIEW

Jayasheel O. Eshcol and Adnan K. Chhatriwalla.

Selective Coronary Angiography Following Cardiac Arrest

RESEARCH PAPER

Qing Zhu, Shasha Liu, Mulalibieke Heizhati, Xiaoguang Yao, Menghui
Wang, Qin Luo, Lei Wang, Delian Zhang, Guijuan Chang, and Nanfang Li.

Systemic Vasculitis: An Important and Underestimated Cause of Malignant Hypertension

REVIEWS

C. Richard Conti

What to Do with Epicardial Coronary Artery Abnormalities That do not Result in Myocardial Ischemia?

Keng Tat Koh, Asri Said, Khaw Chee Sin, Oon Yen Yee, Erwin Mulia, Tan Chen Ting, Francis Shu Eng Pbeng , Ho Kian Hui, Voon Chi Yen, Cham Yee Ling, Khiew Ning Zan, Nor Hanim Mohd Amin, Alan Fong Yean Yip, and Ong Tiong Kiam.

Predictive Value of Resting Pd/Pa for Fractional Flow Reserve Assessed with Monorail Pressure Microcatheter in Real-World Practice

C. Richard Conti, Jamie. B Conti, and Jeff Plasschaert.

Cardiac Rehabilitation: Preliminary Results

Xiaoyu Zheng, Qingyao Liao, Yue Wang, Hua Li, Xiaodong Wang, Yaohui Wang, Wentao Wu, Junlin Wang, Ling Xiao, and Jing Huang.

Ultrasound: The Potential Power for Cardiovascular Disease Therapy (http://ow.ly/LXXH30pllby)

Ömer ?at?ro?lu, Murtaza Emre Durako?lugil, Hüseyin Avni Uydu, Hakan Duman, Mustafa Çetin, Yüksel Çiçek, and Turan Erdo?an.

The Relationship Between Mean Platelet Volume and In-Hospital Mortality in Geriatric Patients with ST Segment Elevation Myocardial Infarction Who Underwent Primary Percutaneous Coronary Intervention

CASE REPORTS

Andreas Seitz, Sophie Schäfer, Maik Backes, Heiko Mahrholdt, and Peter Ong.

Giant Aneurysm of a Coronary-Pulmonary Artery Fistula: A Rare Cause of a Diastolic Murmur

Steven J. Ross, Sahil Prasada, Hassan Ashraf, David Wymer, and C. Richard Conti.

Superior Vena Cava Occlusion as a Complication of Transvenous Cardiac Device Implantation: A Case Report and Brief Review

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Cardiovascular Innovations and Applications

Analysis of sex disparities in ophthalmic research

What The Study Did: Sex disparities in ophthalmic research were analyzed in this study that evaluated the representation of female authorships in ophthalmologic journals from 2008 to 2018, with sex assigned according to first name.

Authors: Michael H. K. Bendels, M.D., Ph.D., of Goethe-University in Frankfurt, Germany, is the corresponding author.

(doi:10.1001/jamaophthalmol.2019.3095)

Editor's Note: The article contains conflict of interest disclosures. Please see the article for additional information, including other authors, author contributions and affiliations, financial disclosures, funding and support, etc.

Credit: 
JAMA Network

Sensory impairment and health expectancy in older adults

Out of the five physical senses, impairment in vision and hearing, especially simultaneously, may have the greatest impact on the health of older adults. These impairments are associated with poor health outcomes, such as limitations in physical function and activities of daily living (ADLs), social isolation, cognitive decline, depression, poor self-rated health (SRH), communication difficulties, and even mortality. Studying the effect of vision and hearing impairment on life expectancy and health expectancy - the duration of remaining life expected to be spent with (or without) health problems - in older adults is relevant because these impairments affect both the quality and the quantity of life. This would allow care providers, policy makers and older adults and their families to thoroughly understand the impact of these common, yet often treatable, impairments.

"We investigated how vision and hearing impairments impact life expectancy and health expectancy among older adults. We were specifically interested in understanding how these impairments affect health expectancy when health is defined by a) physical function and b) the ability to perform activities of daily living (ADLs) - two important health indicators among older adults," said Dr Rahul Malhotra, Head of Research, Centre for Ageing Research and Education, Duke-NUS, and senior author of the study. Dr Malhotra is also an Assistant Professor with the Duke-NUS Health Services and Systems Research Programme (HSSR).

The researchers asked participants to rate their own vision and hearing abilities. To assess physical function, they asked participants to report whether they had trouble with tasks involving their arms and legs, such as walking 200-300 metres, climbing ten steps without resting, or raising their hands above their heads. They also asked participants to report whether they had trouble completing basic ADLs, including bathing, dressing or eating, or instrumental ADLs, such as doing housework, managing their medications or taking public transport.

They found that, at ages 60, 70 and 80, people with either or both vision and hearing impairments could expect more years of remaining life with limited physical function as well as with limitations in ADLs, compared to those without impairments.

People with both hearing and vision impairments had the greatest reduction in health expectancy, as well as an overall lower life expectancy. For example, at age 60, those with both impairments could expect not only a life expectancy that was about four years shorter than unencumbered participants, but also about three more years of life with limitation in physical function. Older adults with both impairments could expect to spend 62% of their remaining life with limitation to physical function, while the estimated figure for those with neither impairment was 38%. In addition, older adults with both impairments could expect to spend nearly one-third (31%) of their remaining life with limitation in ADLs, while those with neither impairment could expect only 16%.

"What's unique about our study is that we allowed vision and hearing impairment status to vary over time in the analysis. This is reflective of real-life cases, where some people would progress in their impairment over time, while others would remain stable or improve upon treatment of the underlying cause. We also accounted for the respondents' existing chronic diseases," said Dr Chan Wei-Ming Angelique, Executive Director, Centre for Ageing Research and Education, Duke-NUS, and co-author of the study. Dr Chan is also an Associate Professor with the Duke-NUS' HSSR.

"Vision and hearing impairments are often perceived as an unfortunate but inconsequential part of ageing, and in many cases, remain undetected or untreated. This important study by our researchers shows that early detection and timely management of vision and hearing impairments by older adults, their families and health systems are key to increasing the quality of life for older adults," said Professor Patrick Casey, Senior Vice Dean for Research at Duke-NUS.

The team is planning to compare this study's findings, which was based on self-reported vision and hearing impairment, with objectively measured impairment status by other groups in Singapore and around the world.

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Duke-NUS Medical School

Wiggling it beats a path for a better performance at school

video: Marching, wiggling and tapping a beat aids young children to develop their self-regulation skills and improve school readiness.

Image: 
QUT Media

Marching, wiggling and tapping a beat aids young children to develop their self-regulation skills and improve school readiness, as shown in newly-published QUT early childhood research.

Associate Professor Kate Williams designed a low-cost preschool program focusing exclusively on rhythm and movement activities linked to pathways in the brain to support attentional and emotional development.

"Think heads, shoulders, knees and toes but do the actions backwards while you sing forwards. It tricks the brain into gear," Assoc Prof Williams said.

The Queensland study, involving 113 children from lower socioeconomic communities, measured the effectiveness of the program to boost self-regulation skills.

"Being able to control your own emotions, cognition and behaviours is an important predictor of school readiness and early school achievement," Assoc Prof Williams said.

"The aim is for regular sessions to be introduced into daily activities of young children to help support their attentional and emotional regulation skills, inhibition and working memory. We want all early childhood teachers to feel confident to run these fun and important activities."

The findings have been published in the international peer-reviewed journal Psychology of Music.

The study is a unique investigation about preschool children and the application of a rhythm and movement program to address socioeconomic-related school readiness and achievement gaps.

Assoc Prof Williams said differences in neurological processes can produce educational inequalities for young children who experience disadvantage. It's been identified by UNICEF as an international priority.

The study recognises what Assoc Prof Williams describes as the 'musician advantage' - enhanced neural plasticity and executive functioning - particularly among children given formal musical instruction.

"The children who have music lessons from a young age are often from families who can afford them," she said.

"The problem is that the children who most need the musician advantage miss out because it isn't affordable for all families to access highly quality music programs".

She said the benefits of early shared book reading between parents and children have long been established.

Another recent Australian study, led by Assoc Prof Williams, was the first to show that early shared music activities in the home also contributed to positive development.

The preschool program involved group sessions for 30 minutes twice a week across eight weeks, with stages becoming more challenging to stimulate change and development in self-regulation skills.

Credit: 
Queensland University of Technology

Financial abuse of older adults by family members more common than scams by strangers

image: This is Duke Han, PhD, associate professor of family medicine, Keck School of Medicine of USC.

Image: 
Ricardo Carrasco III

LOS ANGELES — Despite numerous telephone, mail and internet scams directed toward older adults, relatives may perpetrate more financial elder abuse than strangers, suggests a new study by experts at the Keck School of Medicine of USC.

Using a unique source of frontline data — instances of elder abuse reported to the National Center on Elder Abuse (NCEA) resource line, Keck School researchers were able to identify the most common types of elder abuse reported and profile the alleged perpetrators. The NCEA resource line is a source for individuals seeking information regarding how to identify or report elder abuse.

Of the nearly 2,000 calls logged for the study, more than 42% (818 calls) alleged abuse. Financial abuse was the most commonly reported at nearly 55% (449 calls).

Family members were the most frequently identified perpetrators of alleged abuse at nearly 48% of calls in which relationship could be determined. The most common abuse perpetrated by family was financial abuse (61.8%), followed by emotional abuse (35%), neglect (20.1%), physical abuse (12%) and sexual abuse (0.3%). Of the calls that alleged abuse by a family member, more than 32% reported more than one abuse type.

"We expected to find that financial abuse was the most common abuse reported," says Gali Weissberger, PhD, lead author of the study, and postdoctoral scholar in the Han Research Lab at the Keck School. "But despite the high rates of financial exploitation perpetrated by scammers targeting older adults, we found that family members were the most commonly alleged perpetrators of financial abuse. In fact, across all abuse types, with the exception of sexual abuse and self-neglect, abuse by a family member was the most commonly reported."

Elder abuse affects an estimated one in 10 older adults annually, but is often underreported. Aside from its physical, psychological and social impact on victims, their families and society, elder abuse attributes to more than $5.3 billion in U.S. annual health care costs.

"This is the first study to characterize elder abuse from calls made to the NCEA resource line, which serves as a public access point for people seeking information and resources about elder abuse," says Duke Han, PhD, associate professor of family medicine at the Keck School and corresponding author of the study. "Our findings highlight the importance of resource lines for those seeking information on elder abuse, as many calls were made to understand whether certain situations reflected abuse."

The researchers coded nearly 2,000 calls, emails or messages logged on the NCEA hotline between August 2014 and June 2017, reviewing for any mention of abuse. They categorized type of abuse alleged, whether multiple types of abuse occurred and who perpetrated the alleged abuse.

The researchers add that it is important to incorporate diverse data sources when collecting information regarding alleged abuse. The study was limited by selection bias, as the data was from individuals proactively calling the NCEA line.

"The results highlight the importance of developing effective strategies to prevent future abuse," says Weissberger. "Our next step is to conduct more studies targeting high-risk individuals and to better understand additional risk factors."

Credit: 
University of Southern California - Health Sciences

Drug accelerates blood system's recovery after chemotherapy, radiation

image: Dr. John Chute

Image: 
UCLA Broad Stem Cell Research Center

A drug developed by UCLA physician-scientists and chemists speeds up the regeneration of mouse and human blood stem cells after exposure to radiation. If the results can be replicated in humans, the compound could help people recover quicker from chemotherapy, radiation and bone marrow transplants.

The study, published in Nature Communications, also sheds light on the basic biology behind blood stem cell regeneration and the role of a specific molecular process that is blocked by the new drug. Blood stem cells reside in the bone marrow and produce all of the body's blood and immune cells.

"We're very excited about the potential medical applications of these findings," said Dr. John Chute, a member of the Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research at UCLA and a professor of medicine and radiation oncology in the division of hematology/oncology at the David Geffen School of Medicine at UCLA.

Previous research has shown that a protein called receptor type protein tyrosine phosphatase-sigma, also known as PTP-sigma, is found mostly in the nervous system, where it controls the regeneration of neurons. When PTP-sigma is activated in neurons, it puts the brakes on neuron regeneration; without PTP-sigma, nerves regenerate more easily after an injury.

Chemotherapy and radiation generally suppress the activity of blood stem cells, and it typically takes weeks or months for the blood and immune systems to recover. In 2014, Chute and his colleagues discovered that PTP-sigma is also present on blood stem cells, and that its role in blood stem cells is similar to its function in neurons. In that study, the scientists found that in mice with a PTP-sigma gene deficiency, blood stem cells regenerated faster after they were suppressed by radiation.

PTP-sigma belongs to a group of proteins called tyrosine phosphatases that are notoriously hard to block with drugs. Most tyrosine phosphatases have similar active sites -- the part of the protein that interacts with other molecules to do its job. So drugs that block the active site of one tyrosine phosphatase commonly block other tyrosine phosphatases at the same time, causing a range of side effects.

For the new study, Chute collaborated with Michael Jung, the UC Presidential Chair in Medicinal Chemistry and UCLA distinguished professor of chemistry and biochemistry, and an expert in drug development. Jung's team designed and synthesized more than 100 candidate drugs to block PTP-sigma; Chute and his team tested the candidates for function. Several of the candidate drugs blocked PTP-sigma, with no effects on other phosphatases.

Chute's team tested numerous variations of the drug candidates on human blood stem cells in lab dishes and on mouse blood stem cells to determine which was most effective at accelerating the recovery of blood stem cells after radiation.

One compound, DJ009, emerged as the winner. DJ009 enabled the human blood stem cells to recover while they were in the lab dishes. Those human blood stem cells were then transplanted into immune-deficient mice, where the cells were able to survive and function properly. Chute said that finding indicates that the drug could work eventually work in humans.

"The potency of this compound in animal models was very high," said Chute, who is also a member of the UCLA Jonsson Comprehensive Cancer Center. "It accelerated the recovery of blood stem cells, white blood cells and other components of the blood system necessary for survival. If found to be safe in humans, it could lessen infections and allow people to be discharged from the hospital earlier.

Of the mice that received high doses of radiation, nearly all of the mice that were given DJ009 survived; more than half of those that did not receive the PTP-sigma inhibitor died within three weeks.

In mice that received chemotherapy -- at doses approximating those used in people with cancer -- mice that didn't receive DJ009 had dangerously low levels of white blood cells and neutrophils, the cells that fight bacteria, after two weeks; in mice treated with the PTP-sigma inhibitor, white blood cell counts had already recovered to normal levels.

The researchers are now working to fine-tune DJ009 and other similar compounds so they can move toward human trials. They also are continuing to explore the mechanisms through which inhibiting PTP-sigma promotes the regeneration of blood stem cells.

The experimental drugs that inhibit PTP-sigma were used in preclinical tests only and have not been tested in humans or approved by the Food and Drug Administration as safe and effective for use in humans.

Credit: 
University of California - Los Angeles Health Sciences

Advanced data analysis enhances precision medicine application in clinics

image: Pregnant woman

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pixabay.com: 1041483

This novel open-source computational framework, combined with targeted high-coverage sequencing data promotes the R&D of Non-Invasive Prenatal genetic Screening (NIPT) to make it completely affordable and routinely applicable in clinics. The developed data analysis method uses high-coverage sequencing data from targeted genomic regions to detect fetal trisomies and the parental origin of the trisomic chromosome from the mother's blood sample in the first trimester of pregnancy.

Estonian researchers from the Competence Centre on Health Technologies (CCHT), University of Tartu and University of Helsinki recently published an article in PLOS ONE, demonstrating a novel computational framework for targeted high-coverage sequencing-based NIPT. This computational analysis framework allows for detection of fetal trisomy and the parental origin of the trisomic chromosome using targeted high-coverage sequencing data of a pregnant patient's blood sample.

The developed framework incorporates two analytical layers. First, sequentially located targeted genomic positions are classified by a hidden Markov model, which has been parameterised using the targets of the normal reference chromosome of the same sample. Next, results of a studied sample are grouped and classified for each studied chromosome (eg. Chr 21, causing Down syndrome) using supplemental machine learning methods, such as decision tree and support vector machine. The final outcome is an estimation of euploidy or trisomy for each studied chromosome.

According to the lead author of the study, senior researcher Dr Priit Palta, the developed analytical pipeline was the missing part for implementing the novel advanced laboratory method called TAC-seq for NIPT applications. "NIPT data analysis and foetus trisomy detection based on the mother's blood sample is always a challenging task. We now have both - laboratory and computational tools for developing and providing more feasible and cost-effective NIPT applications that have potential in clinical practice".

Multiple previously developed NIPT tests are based on whole-genome sequencing. Although the entire genome is covered at ultra-low sequencing depth, it is still a resource-demanding approach. The latter is reflected in the relatively high retail price of NIPT, which for example, is currently available for 250 euros in Estonia. However, targeted sequencing approaches like TAC-seq enable to focus only on the relevant chromosomes or regions of the genome, allowing processing more samples in parallel. In addition to reduced sequencing demand, robust cell-free DNA library preparation further decreases the overall NIPT cost per sample.

The head of CCHT NIPT service and R&D laboratory, Dr Kaarel Krjutškov, noted that NIPT is a perfect example of much-praised precision medicine, which is already available and used daily in clinical practice. "Blood origin cell-free DNA sequencing is the core technology for NIPT assays. Sequencing itself is an extremely powerful method for analysing the content and quantity of DNA strands. Now, applying this novel computational method, we can develop cheaper targeted assays in order to read out more from the sequencing data of studied samples, increasing the usefulness of cell-free DNA sequencing and improving the quality of pregnancy-related healthcare in the near future".

Credit: 
Estonian Research Council

Monster penguin find in Waipara, New Zealand

image: Drs Vanesa De Pietri, Paul Scofield and Gerald Mayr examine a Crossvallia waiparensis fossil at Canterbury Museum.

Image: 
Canterbury Museum CC BY NC

A new species of giant penguin - about 1.6 metres tall - has been identified from fossils found in Waipara, North Canterbury.

The discovery of Crossvallia waiparensis, a monster penguin from the Paleocene Epoch (between 66 and 56 million years ago), adds to the list of gigantic, but extinct, New Zealand fauna. These include the world's largest parrot, a giant eagle, giant burrowing bat, the moa and other giant penguins.

C. waiparensis is one of the world's oldest known penguin species and also one of the largest - taller even than today's 1.2 metre Emperor Penguin - and weighing up to 70 to 80 kg.

A team comprising Canterbury Museum curators Dr Paul Scofield and Dr Vanesa De Pietri, and Dr Gerald Mayr of Senckenberg Natural History Museum in Frankfurt, Germany, analysed the bones and concluded they belonged to a previously unknown penguin species.

In a paper published this week in Alcheringa: An Australasian Journal of Palaeontology, the team concluded that the closest known relative of C. waiparensis is a fellow Paleocene species Crossvallia unienwillia, which was identified from a fossilised partial skeleton found in the Cross Valley in Antarctica in 2000.

Canterbury Museum Senior Curator Natural History Dr Paul Scofield says finding closely related birds in New Zealand and Antarctica shows our close connection to the icy continent.

"When the Crossvallia species were alive, New Zealand and Antarctica were very different from today - Antarctica was covered in forest and both had much warmer climates," he says.

The leg bones of both Crossvallia penguins suggest their feet played a greater role in swimming than those of modern penguins, or that they hadn't yet adapted to standing upright like modern penguins.

C. waiparensis is the fifth ancient penguin species described from fossils uncovered at the Waipara Greensand site.

Dr Gerald Mayr says the Waipara Greensand is arguably the world's most significant site for penguin fossils from the Paleocene Epoch. "The fossils discovered there have made our understanding of penguin evolution a whole lot clearer," he says. "There's more to come, too - more fossils which we think represent new species are still awaiting description."

Dr Vanesa De Pietri, Canterbury Museum Research Curator Natural History, says discovering a second giant penguin from the Paleocene Epoch is further evidence that early penguins were huge. "It further reinforces our theory that penguins attained a giant size very early in their evolution," she says.

The fossils of several giant species, including C. waiparensis, will be displayed in a new exhibition about prehistoric New Zealand at Canterbury Museum later this year.

Credit: 
Canterbury Museum

Simple protocol for assessing maturation of HPCs from induced pluripotent stem cells

image: Stem Cells and Development is dedicated to communication and objective analysis of developments in the biology, characteristics, and therapeutic utility of stem cells, especially those of the hematopoietic system.

Image: 
Mary Ann Liebert, Inc., publishers

New Rochelle, NY, August 13, 2019-Researchers have developed a guide to help labs standardize the production of mature hepatic-like cells (HPCs) from stem cells and easily compare gene expression of HPCs to actual human liver tissue. This moderately high throughput protocol can enable a relatively quick assessment of the efficacy of stem cell differentiation and help guide the optimization of differentiation conditions in regenerative medicine applications. The protocol and its implications are published in Stem Cells and Development, a peer-reviewed journal from Mary Ann Liebert, Inc., publishers. Click here to read the full-text article for free on the Stem Cells and Development website.

"Guide to the Assessment of Mature Liver Gene Expression in Stem Cell-Derived Hepatocytes" was coauthored by Stephen Strom, Karolinska Institutet (Stockholm, Sweden) and Alejandro Soto-Gutierrez, University of Pittsburgh (PA), and colleagues from Karolinska Institutet, Royan Institute for Stem Cell Biology (Tehran, Iran), and University of Pittsburgh. The researchers used real time-quantitative polymerase chain reaction (rt-qPCR) to determine the mRNA expression of more than 60 genes expressed in fetal and mature human liver samples, normalized to an internal control. They measured gene expression in iPCs produced in their own lab and in those purchased from commercial labs. Genes evaluated included those for liver-specific plasma proteins, cytochrome P450 enzymes, transporters, multi-drug resistant proteins, and the genes requires for pluripotency and the ability of iPCs to differentiate into different cell types.

Graham C. Parker, PhD, Editor-in-Chief of Stem Cells and Development and The Carman and Ann Adams Department of Pediatrics, Wayne State University School of Medicine, Detroit, MI states: "The ability to direct the differentiation of a stem cell population to a target mature cell type and demonstrate the persistence and validity of that achievement is still beyond the skill of most stem cell biologists, and, more worryingly, the field continues to tolerate the assumption that a given paper has achieved this without proof. In their landmark paper, Stephen Strom and colleagues provide a benchmark technique for other laboratories to compare their stem cell derived hepatocyte-like cells to actual human liver samples."

Credit: 
Mary Ann Liebert, Inc./Genetic Engineering News

Nanoparticle therapy targets lymph node metastases

image: iClusters (red/blue/green circles) enter a tumor through the bloodstream (red vessels), then disassemble into smaller nanoparticle drugs (blue circles) that can pass through lymphatics (green vessels) into lymph nodes and kill metastases.

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<i>ACS Nano</i> <b>2019</b>, DOI: 10.1021/acsnano.9b03472

Metastasis, in which cancer cells break free from the primary tumor and form tumors at other sites, worsens the prognosis for many cancer patients. The lymph nodes -- glands of the immune system located throughout the body -- are typically the traveling cells' first destination. Now, researchers have developed a strategy to target metastases in lymph nodes for destruction, before they can cause cancer at other locations. They report their results in ACS Nano.

Soon after a patient is diagnosed with cancer, they typically undergo lymph node biopsies to determine if their cancer has spread. However, this surgical procedure can cause pain, infection and other problems. Studies have shown that cancer cells travel from tumors to specific lymph nodes primarily through tiny vessels called lymphatics, which carry immune cells and fluid rather than blood. So, a treatment that could be injected into the bloodstream, enter a tumor and then pass through the lymphatics might treat metastases. Hong-Jun Li, Jin-Zhi Du and colleagues had previously developed a nanoparticle delivery tool, called iCluster, that travels through the bloodstream to a tumor. It's a large cluster of nanoparticles, and the acidic environment of the tumor causes iCluster to disassemble into its smaller components, which can penetrate deep into tumors and deliver chemotherapies. But the team wondered whether these smaller nanoparticles could also pass through the lymphatics that connect the tumor to lymph nodes.

To find out, Li, Du and colleagues injected iCluster, labeled with a red dye, into the bloodstream of mice with transplanted tumors. By fluorescent imaging, they observed that small nanoparticles carrying the chemotherapy drug cisplatin could indeed pass through the lymphatics from the tumor to adjoining lymph nodes. In another experiment, the researchers treated mice with primary tumors before metastasis with iCluster, and a couple of days later, surgically removed their primary tumors, similar to what would be done for cancer patients. About 40% of the treated mice were still alive 110 days later. That's in contrast to the untreated mice -- all of them died from metastases within 51 days of surgery. Then, the team tested the therapy on mice that already had metastases. The iCluster-treated mice lived longer, and upon autopsy, had far fewer tumors than untreated mice.

Credit: 
American Chemical Society

Microplastics in arctic snow suggest widespread air pollution

Wind plays a role in carrying microplastics (shreds of plastic less than five millimeters long) to both the snowy streets of European cities and remote areas of the Arctic Ocean - where ecosystems are already stressed by the effects of climate change. The high concentrations found in snow samples from disparate regions suggest microplastics - which may contain varnish, rubber, or chemicals used in synthetic fabrics - cause significant air pollution. What's more, previous studies have shown that microplastics may contribute to lung cancer risk, highlighting an urgent need to further assess the health risks of inhaling them. To better understand how microplastics travel so far, which has been a question, Melanie Bergmann et al. used an imaging technique to analyze snow samples collected between 2015 and 2017 from floating ice in the Fram Strait, a passage between Greenland and Svalbard to the Arctic Ocean. (They visited five ice floes by ship-based helicopters or dinghies during three expeditions.) For comparison, the researchers investigated samples from the remote Swiss Alps and the City of Bremen in northwest Germany. They observed that while concentrations of microplastics in Arctic snow were significantly lower than the concentrations in European snow, the levels of this pollutant in the far North were still substantial. Most of the particles were in the smallest measurable size range of less than 11 micrometers; such particles are more likely to be picked up by atmospheric transport, the authors say. Because most studies currently focus on particles larger than 200 or 300 micrometers, measuring smaller particles remains important, in order to realistically assess microplastics' environmental toll. The high amounts of microplastics in snow, as reported here, suggest that atmospheric transport and deposition could represent a significant pathway for these materials to places far afield, the authors say.

Credit: 
American Association for the Advancement of Science (AAAS)

New 3D interconnection technology for future wearable bioelectronics

image: Figure 1-1 Graphical summary of the work. Carbon nanotubes with platinum (Pt) decoration shows high affinity with liquid metals (left), and it results in the uniform dispersion of carbon nanotubes in liquid metal, forming stretchable metal composite (middle). The stretchable metal composite has superior mechanical properties than pristine liquid metal, and thus fits to be patterned as consistently-fine (i.e. high resolution), 3D structures (right).
Figure 1-2 Photographs of liquid metal (left), liquid metal with carbon nanotubes without platinum (Pt) (middle), stretchable metal composite with Pt decoration on the surface of carbon nanotubes (right). Platinum (Pt) enables the uniform dispersion of carbon nanotubes in liquid metal matrix.

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IBS

It seems the days are gone when just tossing a smart watch on your wrist makes you look cool. The wearable biotech industry has recently revealed its insatiable hunger for futuristic items. Pain relief goggles that monitor brain waves, vital sign monitoring stickers, and even mind reading glasses. They are just few of the latest items discussed at the 2019 Wearable Tech, Digital Health, and Neurotech Silicon Valley conferences. Not to be sure whether all of these wearable prototypes can catch on, but one thing is clear: there are more to come in the field of wearable technology. This great potential has been, however, held back by a technical restraint: these wearables have never really felt "wearable" to their users.

Though they were supposed to feel like a second skin of the wearer, it has been technically impossible to devise "wearable" devices that are comfortable to bend and stretch and also keep good data recording capabilities on soft and curved skin. Wearable smart devices gather a person's bio measurements by connecting electrodes to the surface of the skin. Inside the device are 3D-shaped electrode wirings (i.e. interconnects) that transmit electrical signals. To date, not only can the wirings only be formed on a hard surface, but also the components of such interconnects delicate and hardly-stretchable metals such as gold, copper, and aluminum. In a paper published today in the journal Nano Letters, the joint research team led by Prof. Jang-Ung Park at the Center for Nanomedicine within the Institute for Basic Science (IBS) in Daejeon, South Korea, and Prof. Chang Young Lee at the Ulsan National Institute of Science and Technology (UNIST) in Ulsan, South Korea reported fully-transformable electrode materials that also feature a high electric conductivity. Notably, this novel composite is super-thin, 5 micrometers in diameter, which is half of the width of conventional wire bonding. By enabling ever-slimmer 3D interconnects, this study can help to revolutionize the physical appearance of smart gadgets, in addition to reinforcing their technical functions.

The research team used liquid metals (LM) as the main substrate since LMs are highly stretchable and have relatively high conductivities similar to solid metals. To improve the mechanical stability of the metal liquid, carbon nanotubes (CNT) were dispersed uniformly. "To have a uniform and homogeneous dispersion of CNTs in liquid metal, we selected platinum (Pt), for having a strong affinity to both CNT and LM, as the mixer and it worked," said Young-Geun Park, the first author of the study.

This study also demonstrated a new interconnection technology that can form a highly conductive 3D structure at room temperature: For having a high conductivity, the new system does not require any heating or compressing process. Also the soft and stretchable nature of the new electrode makes it easy to come through the nozzle in a fine diameter. The research team used a nozzle for the direct printing of various 3D patterning structure as shown in Figure 3. Park explains, "Forming high-conductivity 3D interconnections at room temperature is an essential technology that enables the use of various flexible electronic materials. The wire bonding technology used in existing electronic devices forms interconnects using heat, pressure, or ultrasonic waves that can damage soft, skin-like devices. They have been a great challenge in the manufacturing process of high-performance electronic devices." He noted that the pointed nozzle also allows reshaping of the preprinted pattern into various 3D structure, thus having an electrode work like a "switch" to turn on and off power.

Using the direct printing method, the high-resolution 3D printing of this composite forms free-standing, wire-like interconnects. This new stretchable 3D electrical interconnections specifically consist of super-thin wires, as fine as 5 micrometers. Previous studies on stretchable metals have only been able to present wire lines of several hundred micrometers in diameter. The new system is even thinner than the interconnect of conventional wire bonding. Professor Jang-Ung Park, the corresponding author of the study noted, "We may soon be able to say goodbye to those bulky skin-based interfaces as this freely-transformable, super-thin 3D interconnection technology will come as a big breakthrough to the industry's efforts to produce ever compact and slim gadgets." Blurring the boundary between the human body and electric devices, this new technology will facilitate the production of more integrated and higher-performing semiconductor components for use in existing computers and smartphones, as well as for flexible and stretchable electronic devices."

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Institute for Basic Science

New study reveals unique dietary strategy of a tropical marine sponge

image: The sponge Mycale grandis overgrowing coral on the reef in Kāneʻohe Bay.

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Joy Leilei Shih

Research conducted at the University of Hawaiʻi (UH) at Mānoa School of Ocean and Earth Science and Technology (SOEST) on a marine sponge in Kāneʻohe Bay, O?ahu revealed a unique feeding strategy, wherein the sponge animal acquires important components of its diet from symbiotic bacteria living within the sponge.

Coral reefs are one of Hawaiʻi's most important natural resources and support fisheries and the state's economy. Marine sponges are important components of coral reef ecosystems, but in Hawaiʻi, the Indo-Australian sponge Mycale grandis is an invasive alien species that was only first documented in the islands in the late 1990s. M. grandis is now found in and near major harbors of the Main Hawaiian Islands as well as within Kāneʻohe Bay.

Alien and invasive species are one of the threats to endemic and native species, which are vulnerable due to their evolution in the remote archipelago. M. grandis competes with coral for space on the reef, but unlike coral, which build hard rocky substrate with their skeletons, M. grandis is a soft, non-reef building animal and does not provide the same habitat for other reef organisms.

In a study led by Dr. Joy Leilei Shih for her doctoral research at UH Mānoa, the diet of M. grandis sponges collected from Kāneʻohe Bay was elucidated by using a new application of a technique that relies on naturally occurring stable isotopes to understand the origin of specific compounds in the tissues of plants and animals. In this case, the team tested where amino acids, the building blocks of proteins in tissues, in the sponge came from. Did they originate from food caught and filtered from seawater or were they supplied to the sponge from the microbes living within the sponge itself?

When one organism consumes another, elemental properties in the prey are conserved and leave behind a unique chemical pattern with the predator. By assessing the chemical difference between predator and prey tissues, Shih and colleagues found the diet of sponges did not originate from photosynthesizing microbes (such as seen in corals) and M. grandis feeding did not follow general patterns of other multicellular animals. Instead, the isotopic patterns of the sponge and its symbiotic microbes were not different from one another, indicating the sponge obtains nutrition through the uptake of amino acids originating from their symbiotic microbes.

"While we knew that the symbionts of sponges play an important role in their diet, the mechanism by which it occurred was unknown," said Shih. "The only way to produce the observed amino acid isotopic pattern, or fingerprint, if you will, is through the direct transfer of amino acids from their symbiotic bacteria."

"The patterns we detected in M. grandis and its symbionts are very interesting, as they suggest sponges may be actively capturing materials in seawater to support the needs of their microbial community, which in turn supply the sponge with essential tissue building blocks," said Dr. Chris Wall, a postdoctoral researcher at UH Mānoa and a co-author on the study.

"The symbiosis we see between the sponge and its microbial community is remarkable," said Shih. "We know that sponges rely on their symbionts for a variety of purposes including chemical defense, metabolite removal, and now we have insight into this well-tuned and efficient feeding strategy and the major role these microbial symbionts play in sponge nutrition. The intimate relationship between sponges and their symbionts developed over their long evolutionary history. Sponges are the oldest multi-cellular animal on earth. That's why they are so well-adapted and resilient."

Marine sponges in Hawaiʻi are not well studied. A study by the Smithsonian Institution-organized MarineGEO Hawaiʻi program in 2017 identified 150 previously unseen sponge species in Hawaiʻi, roughly one third of which are new species. Previously, only about 10 sponge species were known to exist in Kāneʻohe Bay. The researchers' new approach to investigating sponge feeding strategies can be applied to future research on other marine sponges in Hawai'i and elsewhere. Sponges play an important role in the nutrient dynamics of coral reefs, and in the future, sponges may rise to dominate coral reefs as corals decline from direct pressure from human activity and climate change. This work provides new insights into the biology of sponges and shows the importance of marine microbes to the diet of an invasive sponge.

Credit: 
University of Hawaii at Manoa