Culture

New technique to monitor evolution of magnetic disturbances from the Aurora Borealis

University of Warwick researchers link up over a hundred magnetometers to form a 'social network'

Magnetometers 'befriend' each other when the disturbance propagates to them

Space weather results in magnetic disturbances on the ground that can interfere with power distribution and electrical systems

Magnetic disturbances caused by phenomena like the northern lights can be tracked by a 'social network' of ground-based instruments, according to a new study from the University of Warwick.

The researchers, led by Professor Sandra Chapman from the University's Department of Physics, have for the first time characterised the observations from over 100 ground based magnetometers in terms of a time-varying directed network of connections. They monitored the development of geomagnetic substorms using the same mathematics used to study social networks. The magnetometers 'befriend' one another when they see the same signal of a propagating disturbance.

The research, published in the journal Geophysical Research Letters, opens up the opportunity to develop more accurate models of substorms and helps us to understand the impact of space weather on our electrical and communication systems.

The northern lights, or Aurora Borealis, occur when charged particles from our Sun bombard the Earth's magnetic field. This stores up energy like a battery which it then releases, creating large-scale electrical currents in the ionosphere which generate disturbances of magnetic fields on the ground. Small versions of these substorms are common, but occasionally larger storms will occur that can have a larger impact.

Using over 100 magnetometers that form the SuperMAG Initiative led by Dr Jesper Gjerloev, the researchers used the mathematical concepts from network science to monitor the development of substorms in the arctic auroral region. As a substorm develops and the electrical current in the ionosphere grows, individual magnetometers will register a change in the magnetic field. Pairs of magnetometers became linked when their measurements correlated with each other, expanding their network of 'friends' and allowing the researchers to monitor how the auroral disturbance from the substorm forms and propagates, and how quickly.

Substorms from the Aurora Borealis create an electrical current in the atmosphere that is echoed at ground level. Localised changes in the Earth's magnetic field can disrupt power lines, electronic and communications systems and technologies such as GPS. They are just one form of space weather that affects our planet on a constant basis.

Professor Sandra Chapman from the University of Warwick Department of Physics said: "When talking about space weather, it is useful to provide a single number or rating that indicates how severe it is. To do this, we need to capture the full behaviour of how intense the event is, how widespread spatially, and how rapidly it is changing. Our aim is to use network science to develop useful parameters that do this, encapsulating all the information from 100+ observations.

"SuperMAG is a great example of how essential international co-operation is to solve problems like space weather that are on a planetary scale, using data from stations located in all the countries that abut the Arctic Circle."

ITHACA, N.Y. - Researchers at Cornell University have shown for the first time that it is possible to reduce ageist attitudes, prejudices and stereotypes through education and intergenerational contact.

Ageism is the most socially acceptable prejudice on the planet, according to the World Health Organization (WHO). Discrimination against a person because of their age is more normalized than even racism or sexism. The WHO, which recruited the Cornell-led team to do the study, will use the research to inform its anti-ageism strategy.

According to the team of researchers, programs that foster intergenerational contact, combined with education about the aging process and its misconceptions, worked best at reducing ageist attitudes. The interventions had the greatest impact on women, teens and young adults. Their study was published in the American Journal of Public Health.

"The most surprising thing was how well some of these programs worked," said co-author Karl Pillemer, professor of human development at Cornell and gerontology in medicine at Weill Cornell Medicine. "If we teach people more about aging - if they're less frightened of it, less negative about it and less uncomfortable interacting with older people - that helps."

Macro- and micro-aggressions, such as workplace discrimination and ageist jokes in movies, can have serious negative effects on the mental and physical health of older people. Physicians with ageist attitudes may misdiagnose their older patients or exclude them from particular treatments.

Older people tend to adopt society's negative attitudes toward aging - and those who do are more likely to experience psychological distress and physical illness. They even die 7.5 years sooner on average than those who have a more positive attitude about aging, Pillemer said.

Researchers analyzed 63 studies, conducted between 1976 and 2018, with a total of 6,124 participants. The studies evaluated three types of interventions that aimed to curb ageism: education, intergenerational contact, and a combination of the two.

The most successful programs combined both education and intergenerational contact. Importantly, Pillemer said, these interventions are both low-cost and easy to replicate.

"Volunteer organizations and after-school programs should think about involving some of these methods to reduce ageist attitudes because they are effective and easy to implement," he said.

The WHO will use the research to create an upcoming global report on ageism.

"We know from past experience that these reports can be particularly effective at raising awareness, generate more political will on a topic and provide an evidence based framework for global and local action," said Alana Officer, who leads the WHO's campaign against ageism. "I hope that the Cornell-led research will help change the world for the better."

Alexandria, Va., USA - At the 97th General Session & Exhibition of the International Association for Dental Research (IADR), held in conjunction with the 48th Annual Meeting of the American Association for Dental Research (AADR) and the 43rd Annual Meeting of the Canadian Association for Dental Research (CADR), many oral and poster presentations centered around temporomandibular disorders, or TMD. The IADR/AADR/CADR General Session & Exhibition is held at the Vancouver Convention Centre West Building in Vancouver, BC, Canada from June 19-22, 2019.

Ji-Woon Park, Seoul National University, Republic of Korea, presented a poster "Autoimmunity May Cause Inflammation and Comorbidities in Temporomandibular Disorders (TMD)." The aim of this study was to investigate the presence of autoantibodies and level of comorbidities in TMD patients and compare their levels according to pain disability groups to seek the possible role of autoimmunity in the etiopathogenesis of TMD pain.

Blood samples from TMD patients were collected. The presence of autoimmune indices and cytokines were analyzed and data were statistically compared between high and low disability groups of the Graded Chronic Pain scale. The results showed a significantly higher level of Immunoglobulin G (IgG) was found in high disability TMD patients along with other autoimmune indices.

Although TMD is associated with low-grade-inflammation, a certain group of patients with elevated IgG levels may show a longer pain duration and higher prevalence of comorbidities. These results may point towards the existence of a nonspecific autoimmune disposition in a subgroup of TMD patients. IgG may be considered as a screening test for the detection of TMD patients with high pain disability levels.

Chandler Pendleton, University of Iowa, Iowa City, USA, presented a poster on "Chair-side TMD Risk Assessment - Result from the OPPERA Dataset." Chair-side risk assessment for TMD is overwhelmingly difficult for dental professionals due to the complex multifactorial biopsychosocial contributions. Pendleton and coauthors developed a simple chair-side risk screening model based on several phenotype characteristics.

Secondary data analysis was performed using the Orofacial Pain: Prospective Evaluation and Risk Assessment (OPPERA) dataset. Three orofacial-related questions and number of comorbidities were determined to be significantly associated with the development of TMD. An increase in the number of orofacial symptoms, the number of different types of headaches in the last year and the number of comorbidities experienced led to an increased hazard of developing TMD. In addition, participants that reported grinding or clenching their teeth during most of the day or all of the time were at an increased hazard of developing TMD.

The results show that the number of both pre-clinical orofacial symptoms and comorbidities, multiple types of headaches and frequent daytime teeth grinding and/or clenching activities could be used for chair-side TMD risk assessment and risk screening tools should be further developed to facilitate dental treatment planning regards to TMD.

Poster presentation #1386 "Autoimmunity May Cause Inflammation and Comorbidities in Temporomandibular Disorders" was held on Thursday, June 20, 2019 at 3:45 p.m. and the poster presentation #2060 "Chair-side TMD Risk Assessment - Result from the OPPERA Dataset" was held on Friday, June 21, 2019 in West Exhibition Hall B of the Vancouver Convention Centre West Building, Vancouver, BC, Canada.

Alexandria, Va., USA - At the 97th General Session & Exhibition of the International Association for Dental Research (IADR), held in conjunction with the 48th Annual Meeting of the American Association for Dental Research (AADR) and the 43rd Annual Meeting of the Canadian Association for Dental Research (CADR),

Stephanie Ortiz, Oregon Health & Science University, Portland, USA, gave a poster presentation on "Gender-specific Differences in the Salivary Microbiome of Caries-active Children." The IADR/AADR/CADR General Session & Exhibition is held at the Vancouver Convention Centre West Building in Vancouver, BC, Canada from June 19-22, 2019.

Dental caries represents one of the most common chronic diseases found in young children and is a multi-factorial disease involving complex interactions of microbiological, genetic and socioeconomic risk factors. While women exhibit higher caries incidence than men, it is unclear if this disparity can be extended to children. Ortiz and coauthors sought to determine gender-specific differences in the salivary microbiome within caries-active children by collecting and testing saliva specimens.

Saliva specimens were collected from 85 children, 41 boys and 44 girls, between the ages of two to 14 years. Microbial DNA was isolated using the QIAsymphony isolation robot and then subjected to PCR amplification using V3-V4 16S rDNA-specific primers and next generation sequencing with high-throughput Illumina sequencing. Oral microbiota libraries and profiles were generated by the Forsyth Institute, Cambridge, MA and subjected to further biostatistical analyses at Oregon Health & Science University, Portland, USA.

Significant differences in oral microbiota were found between caries-active boys versus girls. The primary microbial genera associated with caries in young children includes Actinobaculum, Atopobium, Aggregatibacter and Streptococcus. Actinobaculum, Veillonella parvula and the acid-generating Lactococcus lactis, all microorganisms associated with dental caries, were found in much higher prevalence in caries-active girls than boys, indicating that these microorganisms may play a more significant role in girls to shape the cariogenic microbial environment

This poster presentation, #2780, was held on Friday, June 21, 2019 at 3:45 p.m. in West Exhibition Hall B of the Vancouver Convention Centre West Building, Vancouver, BC, Canada.

Andrey Savchenko, Professor at the Higher School of Economics (HSE University), has developed a method that can help to enhance image identification on videos. In his project, a network was taught by a new algorithm and can now make decisions on image recognition and classification at a rate 10 times faster than before. This research was presented in the paper 'Sequential three-way decisions in multi-category image recognition with deep features based on distance factor' published in Information Sciences.

The neural networks learned to identify humans and animals in videos a long time ago. Artificial neurons can learn by remembering what a certain object looks like in an image. Usually, researchers take an open database of photos (e.g., ImageNet, Places, etc.) and use it to teach a neural network. To speed up the decision-making process, our algorithm is set to pick only some of the sample images, or focus on a limited number of traits. Complications may arise when objects of different classes are in the same photo, and there are only small number of training examples for each category.

The new algorithm now can recognize images without significant accuracy degradation through the application of a sequential three-way decision-making method. By employing this approach, a neural network can analyze simple images in one way for clearly recognizable objects, while objects that are difficult to identify can be given a more detailed examination.

'Each photo can be described by literally thousands of features. So, it wouldn't make much sense to compare all of the features of a given input image with those of a basic training example, since most samples would not be similar to the analyzed image. So, we initially only compared just a few of the important features, and put aside the training instances, which obviously cannot be treated as final solutions. As a result, the training sample becomes smaller and only a few examples are left. At the next stage, we would increase the number of features for the remaining images, and then repeat this process until only one class is left,' Prof. Savchenko noted.

This approach reduced the time for recognition by 1.5 to 10 times, as compared to regular classifiers and known multi-category sequential three-way decisions. As a result, this technology could be used in future on mobile devices and other basic gadgets.

A team of researchers has carried out a detailed study of the genomes of ruminants, giving new insight into their evolution and success.

Ruminants including deer and antelope, as well as sheep, goats, cattle and their wild relatives, have thrived in many ecosystems around the globe. They range in size from the tiny lesser mouse deer of Malaysia to the towering African giraffe.

The new study published today (June 21) in Science and led by Wen Wang and Guojie Zhang at the Kunming Institute of Zoology, and Rasmus Heller at the University of Copenhagen, Denmark, included Professor Harris Lewin at the UC Davis Department of Evolution and Ecology and Genome Center.

Ruminants form an important part of U.S. and world agricultural systems. Farms and ranches have an estimated 95 million cattle in the U.S. alone, along with an estimated 5.2 million sheep and 2 million goats.

"As ecosystems around the world begin to show the impact of climate change, knowing what the genes and their variants are can help with conservation efforts of threatened and endangered ruminant species. It can also provide resources to help mitigate the effects of climate change on agricultural commodities, such as breeding cattle, to be more adapted to warmer, drier climates," said Lewin.

The team generated more than 40 trillion base pairs of raw DNA sequences and assembled them into genomes for 44 species. Based on this data they were able to create a new family tree for ruminants -- placing the largest (giraffe) and smallest (lesser mouse deer) on some of the earliest branches after ruminants emerged as a group 32 to 39 million years ago.

"The data produced in this study provides a foundational genomic roadmap for this ecologically and economically important group of mammals," said Lewin, who also chairs the Earth BioGenome Project, a global effort to sequence the genetic code of all the planet's eukaryotes -- some 1.5 million known species, including all plants, animals, protozoa and fungi. "It is a tremendous resource not only for understanding how evolution has shaped ruminants, but also for understanding the basis of both desirable and undesirable traits, such as inherited diseases."

Genes for a unique digestive system

All ruminants have a specialized, multichambered stomach that allows them to ferment the plants they eat using microbes and to bring material up for further chewing, aiding digestion. This highly specialized digestive system allows ruminants to make the most of a diet high in otherwise-indigestible cellulose.

The study showed that, among the 295 newly evolved genes identified in ruminants, many were associated with the digestive system, such as the structure and function of the compartmented stomach -- the rumen, omasum and abomasum.

The team also identified a number of genes associated with horns and antlers. Ruminants typically have horns or antlers that can play a role in defense or mating behavior.

The researchers were also able to pinpoint evolutionary changes at the species level. As the tallest terrestrial animal, giraffes have a distinct stature and body shape, which likely are adaptions to their savanna habitat. The researchers found that among the 366 genes related to bone development, 115 genes had giraffe-specific mutations.

The ruminant genomes may also hold evidence of humans' impact on these animals. When the researchers used a method to infer past population size, they found massive declines for more than half the species from 100,000 to 50,000 years ago -- around the time modern humans left Africa and spread around the world.

The researchers have created the Ruminant Genome Database, a public collection of the genomic and transcriptomic data presented in their study.

The work was supported by a number of agencies and foundations in China, Europe and the U.S. The UC Davis portion was funded by the U.S. Department of Agriculture and the Robert and Rosabel Osborne Endowment.

Full list of funders: Talents Team Construction Fund of Northwestern Polytechnical University, Strategic Priority Research Program of CAS, National Program for Support of Top-notch Young Professionals, Villum Foundation, Lundbeck Fellowship, Carlsberg Foundation, National Natural Science Foundation of China, Fundamental Research Funds for the Central Universities, Natural Science Foundation of China, Natural Science foundation from Jilin province, Central Public-interest Scientific Institution Basal Research Fund, Danish National Research Foundation, Robert and Rosabel Osborne Endowment, U.S. Department of Agriculture, U.S. National Science Foundation, San Diego Zoo Global, John and Beverly Stauffer Foundation

Recent research suggests that increased visceral fat - that is body fat surrounding a number of important internal organs such as the liver, pancreas and intestines - carries the risk of cognitive impairment in later life. "Our goal was to investigate whether excess organ fat is associated with a reduction in the structural networks and storage capacity of our brain throughout its lifetime. We also wanted to find out whether this interaction can be influenced by oestradiol," said Rachel Zsido.

Oestradiol is a hormone consisting of cholesterol and is the strongest of the three naturally produced oestrogens. It is the most important hormone found in the female body and has many amazing functions - it contributes decisively to the maintenance of the female reproductive system. Men also produce oestradiol, but in much smaller amounts. In both sexes, oestradiol is also produced by fatty tissue, the brain and the walls of blood vessels. It also has a vasodilative and antioxidant effect. Oestradiol can help maintain myelin architecture - and thus the membrane that protects our nerves.

Although visceral fat and estradiol appear to play opposite roles in the healthy ageing process of the brain, it remains unclear how and at what point they interfere with brain structure. To solve this mystery, Zsido and her colleagues examined a large data set of healthy adults aged between 20 and 80, 501 men and 473 women, from the LIFE study. "We looked at the brain structure and body fat of the volunteers on images taken from the magnetic resonance tomograph, as well as their memory and oestradiol levels in the blood. Our results suggest that increased organ fat expands the negative influence of aging on brain networks in men and women. We have also found that men prepare this organ fat earlier, while women are particularly affected in mid-life," the scientist explains.

"The decrease in oestradiol in this middle phase of life accelerates the normal aging process. It seems, however, that oestradiol protects women's brains from structural damage to the gray matter during the middle of life", adds Julia Sacher, who along with her research group is investigating the effects of hormonal changes on mood, emotional well-being and cognition. "We took a closer look at a subgroup of women between the ages of 35 and 55 and found that a low level of oestradiol is associated with weaker memory performance in the middle of life. This is also the age range in which the transition to menopause occurs, which is initially characterised by abrupt oestradiol fluctuations and finally by a stop in the reproductive phase. We therefore believe that the pre-menopausal phase provides an important window of opportunity to prevent accelerated brain aging and the development of neurodegenerative diseases such as dementia or depression in women.

Hormones important in risk recognition for dementia or depression

A second joint study led by Julia Sacher and Steffi Riedel-Heller from the Institute for Social Medicine, Occupational Medicine and Public Health (ISAP) also showed a decisive interaction between unfavourable metabolic states and another important sex hormone, testosterone. The team found that elevated testosterone levels and changes in body weight have different effects on women's susceptibility to depression before and after menopause. "Together, the results from both studies emphasize the need to further consider sex differences and sex hormones when investigating the risk of neurodegenerative diseases," summarizes Julia Sacher. This is particularly important in mid-life, as this transitional phase offers women a special opportunity for prevention.

We usually think that trauma from war is related to the fact that soldiers have been under constant threat of death. New research shows a slightly different picture.

The types of trauma that Norwegian soldiers were exposed to in Afghanistan greatly affected the psychological aftermath of their experiences.

Psychologist Andreas Espetvedt Nordstrand and his research team have looked at how exposure to different types of traumatic experiences influenced Norwegian veterans who were in Afghanistan.

The study shows that being exposed to life-threatening situations results in fewer post-traumatic stress symptoms for soldiers than when they experience suffering and death without being in danger themselves.

Nordstrand is affiliated with the Norwegian University of Science and Technology's (NTNU) Department of Psychology and is one of the authors of the study, published in the European Journal of Psychotraumatology.

The study is part of a comprehensive survey of how veterans are faring after the war in Afghanistan.

Just over 7000 Norwegian soldiers participated in the war in Afghanistan between 2001 and 2011, and 4053 of them participated in this investigation.

Violation of moral principle

Trauma is roughly divided into danger-based and non-danger-based stressors.

Soldiers can be exposed to danger-based trauma in classic military settings, such as being shot or ambushed. It is an active threat that is linked to anxiety.

Non-danger-based trauma is divided into two subgroups:

Witnessing: seeing suffering or death of others, without being in danger oneself.

Moral Challenges: seeing or performing an act that violates a person's own moral beliefs.

"An example of witnessing might be that a suicide bomber triggers a bomb that hurts or kills children and civilians. Then our soldiers come in to clean up or secure the area after the bomb has gone off and experience the devastation," says Nordstrand.

Performing actions that violate moral principles can involve killing an innocent person.

"For example, an officer may order a person shot because it looks as if he is wearing a suicide vest. But then it turns out that he wasn't, and a civilian ends up being killed," he says.

"Another example could be when an officer supervises and instructs an Afghan unit, and then learns that someone in that unit is abusing small children. It can be difficult to intervene in that kind of situation, but easy for a Norwegian officer to think afterwards that he should have done something," Nordstrand explains.

Far more symptoms

There is a marked difference between how danger-based and non-danger-based stressors affect the symptoms of psychological distress.

The study shows that both danger-based and non-danger-based stressors lead to an increase in post-traumatic stress disorder (PTSD). PTSD can involve being hyper-alert, jumpy, sleeping poorly and reliving events after they've happened.

"The experience that lasted a long time and burdened him afterwards was when he went out on the battlefield after a bomb had gone off and found a glittery child's shoe spattered with blood."

But non-danger-based stressors are likely to trigger far more symptoms of psychological distress.

"In our study, we found that depression, chronic sleep disorders and anxiety were much more linked to non-danger-based stressors than having been in fear for one's life," says Nordstrand.

Appreciate life more

The research results also show that exposure to personal life threats often leads to positive personal development. This type of trauma can contribute to the individual appreciating life more, getting closer to relatives and experiencing greater faith in their ability to handle situations.

Non-danger-based stressors, on the other hand, usually lead to negative personal development, where the person values life less, feels more distant from others and has less faith in himself.

Nordstrand said he didn't expect there to be such a big difference.

Nordstrand's idea for the study came to him through his job as a psychologist in the Norwegian Armed Forces stress management service, where he noticed that often other issues than having been shot at were plaguing the soldiers.

"A lot of soldiers told stories of how witnessing someone else's suffering, especially of children who became victims of the war - were tough to work through," says Nordstrand.

One of the soldiers he's followed up with had participated in lots of battles without dwelling on them.

"The experience that stayed with him and burdened him afterwards was when he went out onto the battlefield after a bomb had gone off and found a child's sparkly shoe spattered with blood," the psychologist says.

According to Nordstrand, a lot of people hide their non-danger-based trauma and don't talk about it to their family, friends or colleagues. He thinks this relates to the fact that non-danger-based trauma is often linked to shame and guilt, and that it can be more difficult to talk about than that they were scared in an exchange of fire.

"A lot of soldiers are probably afraid of feeling alienated if they would tell their family and civilian friends of all the horrors they saw and experienced. Such experiences often don't fit very well with the world view we protected Norwegians have," says Nordstrand.

Wants to focus on the spectrum

The researcher hopes the study can help direct attention to the fact that there is a wide range of traumatic experiences. He would like to see the focus be not only on people who have been in life-threatening situations, but also on assistance personnel, police and firefighters who are exposed to non-danger-based stressors in their occupations on a daily basis.

Other studies, including Swedish ones, show that firefighters are a group that is vulnerable to depression and suicide.

"We tend to turn on the blue light and rush to help when someone has been in a life-threatening situation. I think we can do a much better job of helping people by acknowledging that there's a real risk of mental illness after being exposed to non-danger-based trauma. We should develop protocols so that we can capture those who are vulnerable and figure out how we can better utilize our resources," says Nordstrand.

High-resolution microscopic images of the surface of dental enamel of lepidosauria, which is a subclass of reptiles including monitor lizards, iguanas, lizards, and tuatara, allow scientists to determine their dietary habits. The enamel wear patterns reveal significant differences between carnivores and herbivores, but also allow finer distinctions, such as between algae-, fruit-, and mollusk-eating species. These findings are the result of research by a team led by scientists at Johannes Gutenberg University Mainz (JGU). They point out that so far it has always been difficult to make such fine distinctions between dietary behavior on the basis of dental or skeletal remains alone, particularly in the case of extinct species, because in many reptiles the teeth are of similar shape.

As the researchers report in Proceedings of the Royal Society B, they examined the upper teeth of 77 curated reptile specimens found in the wild and belonging to 23 extant species; the specimens were part of the collections of various natural history museums. For some of the samples, the researchers analyzed pieces of jaw containing teeth directly under a confocal microscope, while in other cases they made silicone impressions of the teeth which they then imaged. They created 3D surface models of the teeth and evaluated them with regard to 46 different characteristics, such as the number of furrows in the enamel and their mean depth. As a result, they found out that the animals could be grouped into different dietary categories based on their dental microwear textures. For example, the tooth enamel of carnivores exhibits only a few shallow furrows whereas the enamel of frugivores is very deeply furrowed. "This method was developed based on mammals. We applied it for the first time to reptiles and were able to show that it also works for lepidosauria," stated Dr. Daniela Winkler of the Institute of Geosciences at JGU, lead author of the research paper. This was not necessarily what they had expected: "Reptiles hardly ever chew their food. Most of the time they simply bite off pieces of food and swallow them whole. Thus there was no guarantee that we would find informative traces of wear."

The researchers now hope to be able to use the method to analyze teeth from dinosaurs and synapsids, which are very similar to those of lepidosauria, as well and finally identify the first herbivores among the terrestrial vertebrates. Synapsids are mammal-like reptiles, which inhabited the Earth around 310 million years ago, pre-dating dinosaurs by 70 million years. Some of them evolved from carnivores into herbivores. "This was a key event in evolution," emphasized Winkler. "Our long-term goal is to find out when exactly this happened and in which species."

Researchers from MIPT, Skoltech, the Joint Institute for High Temperatures of the Russian Academy of Sciences, and Lomonosov Moscow State University have offered a new approach to oil composition analysis. They used high temperature and pressure to dissolve oil in water and analyze its composition. The new method is compliant with the green chemistry principle as it makes it possible to avoid using environmentally hazardous solvents. The paper was published in the Analytical and Bioanalytical Chemistry journal.

Crude oil is almost never utilized in its raw form. It is necessary, however, to know its precise composition to make refining as efficient as possible. Crude oil consists of over 100,000 compounds, with the exact composition of the sample varying based on the field it was extracted at. The extreme complexity of crude oil makes it impossible to separate into individual compounds. Heavier fractions, which are nonvolatile at 300 degrees Celsius, are yet to be properly studied. It is known that they consist chiefly of phenols, ketones, carbazoles, pyridines, quinolines, dibenzofurans, and carboxylic acids. In addition to that, crude oil from some fields may also contain sulphuric compounds. Many hydrocarbons have identical formulas, with the same number of carbon, hydrogen, and oxygen atoms, but differ in their arrangements, i.e., they are isomers.

The vastly different structures obviously exhibit different chemical properties. Heavier hydrocarbons consist of many atoms, which means more structural variability for each compound.

Mass spectrometry provides information on the elemental composition of substances and their molecular mass but often fails to distinguish between different isomers. Such information may be obtained through isotope exchange analysis. This method is based on the fact that, depending on which particular compounds constitute crude oil or some other sample, oxygen and hydrogen atoms will take more or less time to be replaced with their isotopes -- essentially the same elements, but with a different mass. Water is the most readily available and the cleanest source of isotopes, but oil is insoluble in water under normal conditions so potent acids and alkali have to be used instead. But acids tend to break down organic compounds, especially at high temperatures, thus altering the sample's composition.

It is known, however, that compounds insoluble in water may be dissolved in superheated, or supercritical, water at temperatures significantly over 100 C, so it was decided to apply this method to crude oil. The researchers proved it was possible to achieve a water-based crude oil solution by increasing the temperature and pressure and analyzed its composition. The sample was heated to 360 C in heavy water (in which the hydrogen is replaced with deuterium) at a pressure above 300 atm for one hour.

The researchers compared mass spectra of the original sample and the sample after the isotope exchange reaction. The data collected helped obtain more information on the structure of the compounds comprising crude oil. This method may be used to study other complex nonpolar compounds at the molecular level.

"Isotope labels may only be incorporated at specific positions in the molecule, similar to the lock-and-key model," said Professor of Skoltech and MIPT Eugene Nikolaev, who also heads the Laboratory of Mass Spectrometry at Skoltech. "We can analyze molecular structure by using high-resolution mass spectrometry to measure the exchange rate even when it is impossible to separate individual compounds and identify their structure with other methods."

"Light crude oil reserves are depleting. Hydrocracking of fuel oil, which is characterized by its highly complex and poorly studied molecular structure, is playing an ever greater role in gasoline production. Hydrocrackers are expensive, they are not produced in Russia, and they require the use of special catalysts. We have found a way to identify furans, pyridines, and naphthenic acids in crude oil without having to resort to the complex distillation process," says Yury Kostyukevich, one of the authors of the paper and a senior researcher at Skoltech and MIPT laboratories. "We hope our research will help better understand crude oil structure and composition, contribute to the development of new catalysts for more efficient oil refining, and enable improved oil quality monitoring in trunk pipeline systems."

The human brain consists of neurons arranged into microscopic columns. The cortex, which is the seat of most cerebral functions and forms the largest part of the brain, is divided into uncountable micro-columns. However, the exact development of this columnar structure is elusive to neuroscientists. A research team led by Makoto Sato, has recently reported their study describing the role of a specific protein in the growth of these columns.

The team spanning across Kanazawa University, Ryukoku University, Tokyo Institute of Technology and Imperial College London, used the Drosophila melanogaster (fruit fly) brain for their experiments. The visual centre of the Drosophila brain bears high structural resemblance to the columnar arrangement of the human one, making it an apposite, yet simple model to study. To first visualize these columns, N-cadherin (Ncad), a protein specific to the nervous system, was mapped. The spatial locations of Ncad revealed that during the larval stage of the fly, the visual centre comprised a donut-like structure. As the fly matured to the pupal stage, these structures started stacking on top of each other and indeed transformed into a three-dimensional column.

The research team then carefully analysed these columns and found the presence of three neuron types, namely, R7, R8 and Mi1 within them. While R7 was concentrated towards the central core of the columns, R8 and Mi1 were arranged towards the periphery. Now that the structural composition was clear, understanding the process of column formation was the next step. It was suspected that Ncad, which was heavily present in the columns, played a role in this regard. When Ncad was measured in all three neuron types, it was found that R7 neurons contained more Ncad than the peripheral neurons. Since Ncad is known to give cells adhesive properties, the team concluded that it was the levels of Ncad which determined the location of each of the neuron types within the columns. Heavily adhesive neurons such as R7 formed the core of the columns.

Lastly, to see whether Ncad directly affected the columnar arrangement, it was either completely removed or greatly increased in the neurons. As expected, manipulation of Ncad disturbed the columnar assembly and positions of the neurons. For example, R7 neurons without any Ncad were no longer within the core. However, when Ncad was greatly increased within them, the R8 and Mi1 neurons extended towards the core, possibly due to the strong adhesive properties of Ncad.

This study revealed the role of an adhesive protein in arranging neurons to form the columnar microstructure of the brain. "[Ncad-dependant] differential adhesion and inter-layer interaction may be the essential mechanism underlying the 3D organization of column formation that is evolutionarily conserved from the fly optic lobe to mammalian brains", conclude the researchers. This discovery can help neuroscientists monitor healthy development of the brain and uncover other molecules involved in the process.

The CRISPR Journal announces the publication of its June 2019 issue. The Journal is dedicated to validating and publishing outstanding research and commentary on all aspects of CRISPR and gene editing, including CRISPR biology, technology, and genome editing, and commentary and debate of key policy, regulatory, and ethical issues affecting the field. The Journal, led by Editor-in-Chief Rodolphe Barrangou, PhD (North Carolina State University) and Executive Editor Dr. Kevin Davies, is published bimonthly in print and online. Visit The CRISPR Journal website for more information.

This press release is copyright Mary Ann Liebert, Inc. Its use is granted only for journalists and news media receiving it directly from The CRISPR Journal. For full-text copies of articles or to arrange interviews with Dr. Barrangou, Dr. Davies, authors, or members of the editorial board, contact Kathryn Ryan at the Publisher.

1. SHERLOCK might solve rapid, portable detection of plant genes using CRISPR-Cas13

Applications of nucleic acid detection systems in agriculture enable trait screening during breeding, pest surveillance, and pathogen identification. Writing in The CRISPR Journal, researchers from Feng Zhang's laboratory at the Broad Institute and co-founders of Sherlock Biosciences, have repurposed their recently described SHERLOCK CRISPR-Cas13 detection system for agricultural applications. The SHERLOCKv2 platform combines same-sample multiplexing, lateral flow visual readouts, quantitation, and amplification of signal detection. This modified tool was used to quantify glyphosate resistance genes in a soybean mixture and detected multiple herbicide resistance and native plant genes within a single reaction. The technology touts speed, portability, and minimal sample preparation, essential characteristics for a range of field technologies.

Corresponding Author: Feng Zhang, Omar Abudayyeh, & Jonathan Gootenberg (Broad Institute of MIT and Harvard)

2. A barcoded library approach for predicting Cas9 specificity

A drawback of CRISPR-Cas9 technology is its propensity to produce unintended genomic cleavage events at sequences that do not match its target. This is of particular concern for CRISPR-based therapies, in which off-target effects could be harmful to patients. Considerable effort has been made in developing a comprehensive understanding of CRISPR nuclease specificity. However, none of these approaches has delivered a model that can accurately predict a CRISPR nuclease's ability to cleave based entirely on the sequences of the guide RNA (gRNA) and target. In this issue of The CRISPR Journal, researchers from Editas Medicine have developed a library-based biochemical assay that directly reports the cleavage efficiency of a particular Cas9-guide complex by measuring both uncleaved and cleaved target molecules over a range of mismatched library members. This is the first off-target in silico model to be based on gRNAs. Their approach is rapid and capable of generating protein- and guide-specific predictions while simultaneously informing on the biophysics of Cas9 binding versus cutting.

Corresponding Author: Barrett Steinberg (Editas Medicine, Cambridge MA, USA)

3. Too Much Compromise in Today's CRISPR Pipelines

It is difficult to describe the rapid adoption of CRISPR technology without sounding hyperbolic. Researchers who recall the early days of next-generation sequencing barely a decade ago are still astounded at the pace in which CRISPR has been adopted. While there is no question that CRISPR is a game-changing approach to biological engineering, it is important to acknowledge that the technology is still in its infancy and therefore, significant gaps remain. Richard Fox, the Executive Director of Data Science at the gene editing company Inscripta, discusses the importance of addressing existing limitations of CRISPR gene editing in order to realize the full potential of this groundbreaking technology.

Corresponding Author: Richard Fox (Inscripta Inc., Boulder, CO, USA)

4. The Human Right to Science: Assessing Legislation on Germline Engineering

Human germline engineering and its international regulation have become a highly controversial and heavily debated subject in light of recent events. In a new perspective in this issue of The CRISPR Journal, Andrea Boggio and colleagues assess national legislation on germline engineering in 18 countries based on human rights law. Currently, there is no international consensus on how germline engineering should be regulated and existing national legislation fails to provide the governance framework necessary to regulate it in the era of CRISPR. The authors advocate for the human right to science as a starting point for building consensus, at the national and international levels, on governing principles to promote responsible scientific and technological advancements.

Corresponding Author: Andrea Boggio (Bryant University, Smithfield, RI, USA)

5. Giving Genome Editing the Fingers: An Interview with Dana Carroll

Biochemist Dana Carroll was instrumental in the development of zinc finger nucleases, a genome editing predecessor of CRISPR-Cas technology. Although Carroll closed his lab at the University of Utah in 2018, he still has significant influence on the genome editing circuit, such as leading community engagement efforts at the Innovative Genomics Institute in San Francisco. Carroll recently joined CRISPR Journal Executive Editor, Kevin Davies, for an exclusive interview in which he reflects on two decades of research advances in genome editing as well as issues currently impacting the scientific community.

Corresponding Author: Kevin Davies (Executive Editor, The CRISPR Journal)

Japanese scientists at Tokyo University of Agriculture and Technology (TUAT), Teikyo University of Science, and Juntendo University have found -- in animal studies -- a close relationship between vortex flow and pressure differences in the ventricles, or lower chambers, of the heart. The new information could inform the development of new markers for cardiovascular dysfunction that can lead to heart failure.

Their findings were published on April, 2019 in the American Journal of Physiology-Heart and Circulatory Physiology.

Every beat of the heart consists of two stages. In the first stage, known as diastole, the left and right lower chambers of the heart (called ventricles) relax and expand, and blood flows into them from the left and right upper chambers (called atrium). Once the ventricles are full of blood, the second stage, known as systole, is triggered. The muscles in the ventricle walls contract and blood is pumped from the left ventricle to the aorta (main artery carrying oxygenated blood to the body), and from the right ventricle to the pulmonary artery (carrying deoxygenated blood back to the lungs).

Diastolic dysfunction is a common heart condition in both domestic animals and humans, particularly among the elderly, where the diastole stage does not function as efficiently as it should. The muscles in the ventricle walls become thickened and stiff, losing their elasticity, and do not relax and expand properly. As a result, the capacity of these chambers to fill up with blood is reduced. This in turn causes blood to accumulate in other areas of the body.

The restriction in flow causes pressure inside the ventricles to build up as blood pumped with the next heartbeat tries to enter the chamber which, due to its inability to expand properly, lacks sufficient capacity to accommodate it all. Diastolic dysfunction is characterized by an increased pressure in the left ventricle as the oxygenated blood returning from the lungs tries to enter. As the surplus blood has to go somewhere, it also causes blood and pressure to build up in the blood vessels around the lungs (pulmonary congestion) or in the vessels returning blood back to the heart (systemic congestion).

In the case of pulmonary congestion, fluid can leak through the vessel membranes into the alveoli (tiny air sacs that allows air exchange) in the lungs, resulting in pulmonary edema -- a condition where oxygenation of the blood is impaired, leading to breathing difficulties and, in severe cases, to potentially fatal diastolic heart failure.

As blood flows from the left atrium into the left ventricle, it forms a swirling mass of fluid known as a vortex ring. In terms of its fluid dynamics, a rotating vortex is believed to flow more efficiently than a straight, steady flow of fluid and therefore assists filling of the left ventricle during diastole. A healthy heart that exerts sufficient suction force typically has a large intraventricular pressure difference, whereas a heart with diastolic dysfunction has a low intraventricular pressure difference.

Previous studies have suggested that diastolic vorticity, or fluid dynamics of the blood in the ventricle, can be used as an indicator of diastolic function. However, the link between intraventricular pressure difference and diastolic vorticity is unclear. It is thought that pressure differences within the ventricles is linked to the formation of vortexes, and that vortex flow could be used as a measure of ventricular relaxation that is associated with heart failure.

For this study, the researchers monitored six healthy anesthetized dogs to determine whether intraventricular fluid dynamics can be assessed clinically using non-invasive imaging techniques, and whether impaired fluid dynamics may be a source of diastolic dysfunction that can lead to heart failure.

"We showed the close relationship of vortex and intraventricular pressure difference and showed that both of them can become new markers of the left ventricular relaxation property," said Ryou Tanaka, Associate Professor in the Department of Veterinary Surgery, Faculty of Veterinary Medicine, TUAT, and co-author of the paper.

Now that the researchers have assessed the relationship between intraventricular pressure differences and vortex flow in healthy canines, their next step is to evaluate intraventricular fluid dynamics in feline cases. According to the authors, these findings suggest that further studies using these indicators on diseased subjects is warranted.

A hydrogen-natural gas blend (HNGB) can be a game changer only if it can be stored safely and used as a sustainable clean energy resource. A recent study has suggested a new strategy for stably storing hydrogen, using natural gas as a stabilizer. The research proposed a practical gas phase modulator based synthesis of HNGB without generating chemical waste after dissociation for the immediate service.

The research team of Professor Jae Woo Lee from the Department of Chemical and Biomolecular Engineering in collaboration with the Gwangju Institute of Science and Technology (GIST) demonstrated that the natural gas modulator based synthesis leads to significantly reduced synthesis pressure simultaneously with the formation of hydrogen clusters in the confined nanoporous cages of clathrate hydrates. This approach minimizes the environmental impact and reduces operation costs since clathrate hydrates do not generate any chemical waste in both the synthesis and decomposition processes.

For the efficient storage and transportation of hydrogen, numerous materials have been investigated. Among others, clathrate hydrates offer distinct benefits. Clathrate hydrates are nanoporous inclusion compounds composed of a 3D network of polyhedral cages made of hydrogen-bonded 'host' water molecules and captured 'guest' gas or liquid molecules.

In this study, the research team used two gases, methane and ethane, which have lower equilibrium conditions compared to hydrogen as thermodynamic stabilizers. As a result, they succeeded in stably storing the hydrogen-natural gas compound in hydrates. According to the composition ratio of methane and ethane, structure I or II hydrates can be formed, both of which can stably store hydrogen-natural gas in low-pressure conditions.

The research team found that two hydrogen molecules are stored in small cages in tuned structure I hydrates, while up to three hydrogen molecules can be stored in both small and large cages in tuned structure II hydrates. Hydrates can store gas up to about 170-times its volume and the natural gas used as thermodynamic stabilizers in this study can also be used as an energy source.

The research team developed technology to produce hydrates from ice, produced hydrogen-natural gas hydrates by substitution, and successfully observed that the tuning phenomenon only occurs when hydrogen is involved in hydrate formation from the start for both structures of hydrates.

They expect that the findings can be applied to not only an energy-efficient gas storage material, but also a smart platform to utilize hydrogen natural gas blends, which can serve as a new alternative energy source with targeted hydrogen contents by designing synthetic pathways of mixed gas hydrates.

The research was published online in Energy Storage Materials on June 6, with the title 'One-step formation of hydrogen clusters in clathrate hydrates stabilized via natural gas blending'.

Professor Lee said, "HNGB will utilize the existing natural gas infrastructure for transportation, so it is very likely that we can commercialize this hydrate system. We are investigating the kinetic performance through a follow-up strategy to increase the volume of gas storage.

Researchers at The Westmead Institute for Medical Research have discovered brand new immune cells that are at the frontline of HIV infection. Known as CD11c+ dendritic cells, these new cells are more susceptible to HIV infection and can then transmit the virus to other cells.

CD11c+ dendritic cells are a subset of dendritic cells (a type of immune cell) that are only found in human genital tissues, specifically at the epithelial level (the thin layer of tissue that forms the surface) of the vagina, inner foreskin and anus. This location in genital tissue often means that these newly discovered CD11c+ dendritic cells are the first immune cells to interact with HIV.

One of the lead researchers on this project, Associate Professor Andrew Harman from The Westmead Institute for Medical Research says that the role of these newly discovered CD11c+ dendritic cells is to capture any incoming disease-causing virus or bacteria (pathogen), and then deliver it to CD4 T cells.

"CD4 T cells are responsible for driving an immune response to the pathogen. Interestingly, they are also the primary HIV target cells in which the virus replicates.

"Once dendritic cells capture a pathogen, they communicate what they have found to CD4 T cells in the lymph nodes, essentially giving the immune system a constant update. This information prepares the immune system to either tolerate a bacteria or virus, or attack it.

"However, if CD4 T cells fall below critical levels (e.g. in HIV positive patients), then the body is no longer able to mount an immune response, leading to a diagnosis of AIDS.

"Our research team has shown that the newly discovered CD11c+ dendritic cells are more susceptible to HIV infection than any other known dendritic cell. We have also shown that CD11c+ dendritic cells interact with CD4 T cells more efficiently than any other dendritic cells. Importantly CD11c+ dendritic cells transfer the virus to CD4 T cells, making them key drivers of HIV infection. As these dendritic cells are so efficient at interacting with CD4 T cells, they are also important vaccine candidates.

The team from The Westmead Institute for Medical Research were able to discover these CD11c+ dendritic cells using donated genital tissues.

Associate Professor Harman says, "We were able to look at the tissue only 30 minutes after it had been surgically removed from the body and also developed ground breaking RNAscope technology which allowed us to watch as living CD11+c dendritic cells took up the virus and delivered it to the CD4 T cells," says Associate Professor Harman.

According to co-lead author and Executive Director of The Westmead Institute for Medical Research, Professor Tony Cunningham, this discovery has unlocked two new avenues for medical researchers to pursue in the search for more effective HIV treatments.

"This finding opens up a potential for the development of strategies to block the transmission of HIV. If we can block HIV's ability to bind to the CD11+c dendritic cells, which are often the first immune cells to encounter the HIV virus, then we can stop their ability to transmit the virus to the CD4T cells. In a situation where there are low levels of CD4 T cells, this could stop the virus from spreading.

"Another avenue is to use this new information to develop a HIV vaccine. If HIV fragments or inactivated HIV were targeted at these CD11+c dendritic cells, this would have the potential to prime an immune response against HIV as soon as it enters the body," says Professor Cunningham.