Genetic Factors Involved in Shaping the Composition of the Human Gut Microbiome (Biology)

Human genes have an impact on shaping our gut ecosystem according to new evidence from the international MIBioGen consortium study involving more than 18,000 people. The findings, led by the University Medical Center Groningen, Netherlands and involving researchers at the University of Bristol, are published today [18 January] in Nature Genetics.

Artist impression of gut © University of Bristol

The last decade has substantially broadened our knowledge of the human microbiome, the microbial ecosystem that inhabit the internal and external surfaces of our bodies. The trillions of microbes living with us are not just passengers ‒ they actively participate in many human functions, helping us to digest food, training our immune system and even affecting our mood via the gut-brain axis.

The largest and richest human microbiome inhabits the gut and contributes substantially to our health. Yet the factors that shape its composition, although widely studied, remain unclear, and the more than 80 per cent difference in gut microbiome between individuals remains unexplained. In general, environmental factors such as diet and medication play a major role, however a role for human genetic variants has also been suggested by the identification of heritable bacteria, i.e. those that are more common in twins and family members.  

Now, a new study from the MiBioGen consortium, a collaboration involving more than 20 labs across the world, highlights the common host genetic factors which influence the composition of the human gut microbiome in more than 18,000 people analysed. They report that at least two human genes have a major impact in shaping our gut ecosystem: the lactase gene (LCT), which influences the abundance of lactose-digesting Bifidobacteria, and the fucosyl transferase (FUT2) gene, which determines the abundance of Ruminococcus torques. They also show that other human genes affecting microbiome composition are involved in important aspects of host metabolism, nutrition and immunity. Their analyses stretch as far as establishing relationships between several bacterial species and human diseases. For example, a higher abundance of Bifidobacterium decreased the risk of the inflammatory bowel disease ulcerative colitis, an observation also reported in previous clinical trials.

“This study is a great example of a large international collaboration and is the first to accurately estimate the effect of host genetics on the gut microbiome,” explained Alexandra Zhernakova, one of the principal investigators leading the consortium. “More genetic effects will likely be identified with increased sample size in future studies, but our multi-centre approach did identify robust loci that are shared across populations. However, further studies in large and more homogenous groups are essential to identify population-specific effects and gene-environmental interactions.”

“It was a challenge to combine datasets from multiple cohorts due to the large technical differences and to biological variations across populations. However, this diversity also brings strength – for example, we could see that genetic variants in the lactase gene determine Bifidobacteria abundance in adults, but not in children, and that this effect is more pronounced in European populations,” says Alex Kurilshikov, the first author of the study. “The large sample size also allowed us to apply genetic methods and show that some bacteria are causal for developing diseases.”

Researchers from Bristol Medical School, Dr David HughesProfessor Nic Timpson and Dr Kaitlin Wade, contributed results from the Flemish Gut Flora Project to the MiBioGen consortium, with collaborators in Belgium (Professor Jeroen Raes and Dr Rodrigo Bacigalupe). The authors also advised on Mendelian randomization analyses, an analytical technique pioneered by Bristol’s Professor George Davey Smith and the Medical Research Council Integrative Epidemiology Unit, to understand the causal links between the host gut microbiome and various health outcomes including cardiovascular disease and diet.

Dr Kaitlin Wade, Lecturer in Epidemiology at Bristol Medical School and one of the study’s authors, added: “Ever increasing genome-wide association studies and consortia, such as MiBioGen, provide greater opportunities to understand host genetic contributions to variation in the human gut microbiome. There is also promise in efforts to interrogate the causal role played by the gut microbiome in human health using methods such as Mendelian randomization. Estimating causal effects remains a complicated process; however, when evidence from studies like this corroborate that obtained with other epidemiological studies, our confidence in how the gut microbiome may be used to prevent or treat disease will improve.”

The MiBioGen researchers have made their results available to other scientists and the scientific community for additional and future analyses. All results are uploaded to http://mibiogen.org, supported by the Genomics Coordination Center in the Department of Genetics, UMCG.

Reference: ‘Large-scale association analyses identify host factors influencing human gut microbiome composition‘ by K Wade et al in Nature Genetics, 2021.

Provided by University of Bristol

Clocking the Movement of Electrons Inside an Atom (Physics)

New technique delivers resolution improvement in ultrafast processes.

Ultrafast science is pursued at the Technical University of Munich (TUM). An international consortium of scientists, initiated by Reinhard Kienberger, Professor of Laser and X-ray Physics several years ago, has made significant measurements in the femtosecond range at the U.S. Stanford Linear Accelerator Center (SLAC).

The inherent delay between the emission of the two types of electron leads to a characteristic ellipse in the analysed data. In principle, the position of individual data points around the ellipse can be read like the hands of a clock to reveal the precise timing of the dynamical processes. © Daniel Haynes / Jörg Harms

X-ray free-electron lasers (XFELs) have delivered intense, ultrashort X-ray pulses in the femtosecond range for over a decade. A femtosecond is equivalent to a millionth of a billionth of a second.

One of the most promising applications of XFELs is in biology, where researchers can capture images down to the atomic scale even before the radiation damage destroys the sample. In physics and chemistry, these X-rays can also shed light on the fastest processes occurring in nature with a shutter speed lasting only one femtosecond.

Measurements on miniscule timescales are particularly difficult

However, on these miniscule timescales, it is extremely difficult to synchronize the X-ray pulse that sparks a reaction in the sample on the one hand and the laser pulse which ‘observes’ it on the other. This problem is called timing jitter, and it is a major hurdle in ongoing efforts to perform time-resolved experiments at XFELs with ever-shorter resolution.

Now, a large international research team has developed a method to get around this problem at XFELs and demonstrated its efficacy by measuring a fundamental decay process in neon gas.

Electrons accelerated by SLAC’s linear accelerator ender the LCLS undulator hall and run a gauntlet of 32 powerful undulators. Each undulator contains 224 magnets whose alternating poles force the electrons to zigzag violently and radiate X-rays. By the time they leave the undulator hall, the X-ray laser pulses are a billion times brighter than beams from traditional synchrotron X-ray sources, opening a new realm of possible experiments and discoveries. Image: Christopher Smith/SLAC National Accelerator Laboratory

Good timing can avoid radiation damage

Many biological systems – and some non-biological ones – suffer damage when they are excited by an X-ray pulse from an XFEL. One of the causes of damage is the process known as Auger decay. The X-ray pulse ejects photoelectrons from the sample, leading to their replacement by electrons in outer shells. As these outer electrons relax, they release energy which can later induce the emission of another electron, known as an Auger electron.

Radiation damage is caused by both the intense X-rays and the continued emission of Auger electrons, which can rapidly degrade the sample. Timing this decay would help to evade radiation damage in experiments studying different molecules. In addition, Auger decay is a key parameter in studies of exotic, highly excited states of matter, which can only be investigated at XFELs.

Research team delivers pioneering and highly accurate approach

To chart Auger decay the scientists used a technique dubbed self-referenced attosecond streaking, which is based on mapping the electrons in thousands of images and deducing when they were emitted based on global trends in the data.

For the first application of their method, the team used neon gas, where the decay timings have been inferred in the past. After exposing both photoelectrons and Auger electrons to an external ‘streaking’ laser pulse, the researchers determined their final kinetic energy in each of tens of thousands of individual measurements.

“Crucially, in each measurement, the Auger electrons always interact with the streaking laser pulse slightly later than the photoelectrons displaced initially, because they are emitted later,“ says Prof. Reinhard Kienberger, who helped to develop the experiment’s design. “This constant factor forms the foundation of the technique.” By combining so many individual observations, the team was able to construct a detailed map of the physical process, and thereby determine the characteristic time delay between the photo- and Auger emission.

Streaking method leads to success

The required high time resolution is made possible by the so-called streaking method. “This technique is successfully applied in our laboratory. In several preliminary papers of our group, we have performed time-resolved measurements on free-electron lasers using the streaking method,” says TUM PhD student Albert Schletter, co-author of the publication. “Using this method, we were able to measure the delay between X-ray ionization and Auger emission in neon gases with the highest precision,” explains lead author Dan Haynes of Hamburg’s Max Planck Institute for the Structure and Dynamics of Matter.

The researchers are hopeful that self-referenced streaking will have a broader impact in the field of ultrafast science. “Self-referenced streaking may facilitate a new class of experiments benefitting from the flexibility and extreme intensity of XFELs without compromising on time resolution,” adds co-author Markus Wurzer, who is a PhD student of Prof. Kienberger.

Publications:

D. C. Haynes, M. Wurzer, A. Schletter, A. Al-Haddad, C. Blaga, C. Bostedt, J. Bozek10, M. Bucher, A. Camper, S. Carron, R. Coffee, J. T. Costello, L. F. DiMauro, Y. Ding, K. Ferguson, I. Grguraš, W. Helml, M. C. Hoffmann, M. Ilchen, S. Jalas, N. M. Kabachnik, A. K. Kazansky, R. Kienberger4 A. R. Maier, T. Maxwell, T. Mazza, M. Meyer, H. Park, J. Robinson, C. Roedig, H. Schlarb, R. Singla, F. Tellkamp, K. Zhang, G. Doumy, C. Behrens, A. L. Cavalieri:
Clocking Auger electrons. In: Nature Physics. https://www.nature.com/articles/s41567-020-01111-0
DOI: 10.1038/s41567-020-01111-0

Provided by Technical University of Munich

Loss of Smell is the Best Sign of COVID-19 (Medicine)

Two international studies confirm that for the majority of patients with respiratory infections who lose the sense of smell, this is due to COVID-19. The disease also often results in both loss of taste and the other senses in the mouth. A researcher from Aarhus University has contributed to the new results.

If you have had COVID-19, then forget about enjoying the smell of freshly made coffee. At any rate, two major international studies document that there is frequently a loss of smell and that this often lasts for a long time in cases of COVID-19

Alexander Wieck Fjaeldstad, is associate professor in olfaction and gustation at Aarhus University, and is behind the Danish part of the study.

The study shows that the average loss of the sense of smell was 79.7 on a scale from 0-100 – which indicates a large to complete sensory loss, says the researcher. In addition, the studies show that the loss of smell is very probably the best predictor of COVID-19 among patients with symptoms of respiratory diseases.

“This emphasises how important it is to be aware of this symptom, as it may be the only symptom of the disease,” says Alexander Wieck Fjaeldstad, who also stresses only around half of patients with a loss of smell have gotten their sense of smell back after forty days.

“This differs from the picture we see with other viral infections and causes long-term discomfort for patients, both in relation to food and social contact, while at the same time causing them worry.”

In addition to the loss of the sense of smell, the sense of taste was also significantly reduced, to 69.0 on a scale from 0-100, just as the remaining sense of feeling in the mouth was also reduced, this time to 37.3 on a scale from 0-100.

“While the loss of smell in itself removes the ability to sense the aroma of food, the simultaneous loss of the other senses make it difficult to register what you’re eating. Putting food in your mouth can therefore become a decidedly unpleasant experience,” explains Alexander Wieck Fjaeldstad.

A total of 23 nationalities and over 4,500 COVID-19 patients from all over the world have responded to the researchers’ questionnaire.

“The study is of interest both to patients suffering sensory loss as well as clinicians and researchers who work with diagnostics and following-up on COVID-19. It shows that the loss of smell is specific to COVID-19, which is both relevant in relation to recognising the infection, and because it indicates that the sense of smell is closely linked to how SARS-CoV-2 infects the body.”

Previously, researchers have based the correlation between COVID-19 and the loss of the chemical senses on smaller studies, while these studies collect large amounts of data from countries all over the world.

“The collaboration on the projects also entails a dialogue between researchers from all over the world, which makes it possible to share knowledge and ideas in order to promote the research field,” says Alexander Wieck Fjaeldstad and continues: “The results are in line with our own national studies and pave the way for future studies on risk factors for permanent sensory loss, along with a better understanding of the consequences of these sensory losses for the patients. Among the aspects being studied are which factors are associated with a milder or briefer loss of the sense of smell and how this loss is associated with the rest of the course of the disease. The collection of data is continuing and will result in additional publications with even more participants.”

Reference: Gerkin RC, Ohla K, Veldhuizen MG, Joseph PV, Kelly CE, Bakke AJ, Steele KE, Farruggia MC, Pellegrino R, Pepino MY, Bouysset C, Soler GM, Pereda-Loth V, Dibattista M, Cooper KW, Croijmans I, Di Pizio A, Ozdener MH, Fjaeldstad AW, Lin C, Sandell MA, Singh PB, Brindha VE, Olsson SB, Saraiva LR, Ahuja G, Alwashahi MK, Bhutani S, D’Errico A, Fornazieri MA, Golebiowski J, Hwang LD, Öztürk L, Roura E, Spinelli S, Whitcroft KL, Faraji F, Fischmeister FP, Heinbockel T, Hsieh JW, Huart C, Konstantinidis I, Menini A, Morini G, Olofsson JK, Philpott CM, Pierron D, Shields VDC, Voznessenskaya VV, Albayay J, Altundag A, Bensafi M, Bock MA, Calcinoni O, Fredborg W, Laudamiel C, Lim J, Lundström JN, Macchi A, Meyer P, Moein ST, Santamaría E, Sengupta D, Dominguez PR, Yanik H, Hummel T, Hayes JE, Reed DR, Niv MY, Munger SD, Parma V; GCCR Group Author. Recent smell loss is the best predictor of COVID-19 among individuals with recent respiratory symptoms. Chem Senses. 2020 Dec 25:bjaa081. doi: 10.1093/chemse/bjaa081. Epub ahead of print. PMID: 33367502.

Provided by Aarhus University

Study Finds COVID-19 Attack On Brain, Not Lungs, Triggers Severe Disease In Mice (Medicine)

Georgia State University biology researchers have found that infecting the nasal passages of mice with the virus that causes COVID-19 led to a rapid, escalating attack on the brain that triggered severe illness, even after the lungs were successfully clearing themselves of the virus.

Illustration of the path that covid-19 can take from the nasal passages into the brain © GSU

Assistant professor Mukesh Kumar, the study’s lead researcher, said the findings have implications for understanding the wide range in symptoms and severity of illness among humans who are infected by SARS-CoV-2, the virus that causes COVID-19.

“Our thinking that it’s more of a respiratory disease is not necessarily true,” Kumar said. “Once it infects the brain it can affect anything because the brain is controlling your lungs, the heart, everything. The brain is a very sensitive organ. It’s the central processor for everything.”

The study, published by the journal “Viruses,” assessed virus levels in multiple organs of the infected mice. A control group of mice received a dose of sterile saline solution in their nasal passages.

Kumar said that early in the pandemic, studies involving mice focused on the animals’ lungs and did not assess whether the virus had invaded the brain. Kumars’ team found that virus levels in the lungs of infected mice peaked three days after infection, then began to decline. However, very high levels of infectious virus were found in the brains of all the affected mice on the fifth and sixth days, which is when symptoms of severe disease became obvious, including labored breathing, disorientation and weakness.

Mukesh Kumar, Assistant Professor Biology ©GSU

The study found virus levels in the brain were about 1,000 times higher than in other parts of the body.

Kumar said the findings could help explain why some COVID-19 patients seem to be on the road to recovery, with improved lung function, only to rapidly relapse and die. His research and other studies suggest the severity of illness and the types of symptoms that different people experience could depend not only on how much virus a person was exposed to, but how it entered their body.

The nasal passages, he said, provide a more direct path to the brain than the mouth. And while the lungs of mice and humans are designed to fend off infections, the brain is ill equipped to do so, Kumar said. Once viral infections reach the brain, they trigger an inflammatory response that can persist indefinitely, causing ongoing damage.

“The brain is one of the regions where virus likes to hide,” he said, because it cannot mount the kind of immune response that can clear viruses from other parts of the body.

“That’s why we’re seeing severe disease and all these multiple symptoms like heart disease, stroke and all these long-haulers with loss of smell, loss of taste,” Kumar said. “All of this has to do with the brain rather than with the lungs.”

Kumar said that COVID-19 survivors whose infections reached their brain are also at increased risk of future health problems, including auto-immune diseases, Parkinson’s, multiple sclerosis and general cognitive decline.

“It’s scary,” Kumar said. “A lot of people think they got COVID and they recovered and now they’re out of the woods. Now I feel like that’s never going to be true. You may never be out of the woods.”

Reference: Pratima Kumari, Hussin A. Rothan, Janhavi P. Natekar et al., “Neuroinvasion and Encephalitis Following Intranasal Inoculation of SARS-CoV-2 in K18-hACE2 Mice”, Viruses 2021, 13(1), 132; https://www.mdpi.com/1999-4915/13/1/132/htm https://doi.org/10.3390/v13010132

Provided by GSU

Light-induced Twisting of Weyl Nodes Switches on Giant Electron Current (Material Science)

Scientists at the U.S. Department of Energy’s Ames Laboratory and collaborators at Brookhaven National Laboratory and the University of Alabama at Birmingham have discovered a new light-induced switch that twists the crystal lattice of the material, switching on a giant electron current that appears to be nearly dissipationless. The discovery was made in a category of topological materials that holds great promise for spintronics, topological effect transistors, and quantum computing.

Schematic of light-induced formation of Weyl points in a Dirac material of ZrTe5. Jigang Wang and collaborators report how coherently twisted lattice motion by laser pulses, i.e., a phononic switch, can control the crystal inversion symmetry and photogenerate giant low dissipation current with an exceptional ballistic transport protected by induced Weyl band topology. © AMES Laboratory

Weyl and Dirac semimetals can host exotic, nearly dissipationless, electron conduction properties that take advantage of the unique state in the crystal lattice and electronic structure of the material that protects the electrons from doing so. These anomalous electron transport channels, protected by symmetry and topology, don’t normally occur in conventional metals such as copper. After decades of being described only in the context of theoretical physics, there is growing interest in fabricating, exploring, refining, and controlling their topologically protected electronic properties for device applications. For example, wide-scale adoption of quantum computing requires building devices in which fragile quantum states are protected from impurities and noisy environments. One approach to achieve this is through the development of topological quantum computation, in which qubits are based on “symmetry-protected” dissipationless electric currents that are immune to noise.

“Light-induced lattice twisting, or a phononic switch, can control the crystal inversion symmetry and photogenerate giant electric current with very small resistance,” said Jigang Wang, senior scientist at Ames Laboratory and professor of physics at Iowa State University. “This new control principle does not require static electric or magnetic fields, and has much faster speeds and lower energy cost.”

“This finding could be extended to a new quantum computing principle based on the chiral physics and dissipationless energy transport, which may run much faster speeds, lower energy cost and high operation temperature.” said Liang Luo, a scientist at Ames Laboratory and first author of the paper. 

Wang, Luo, and their colleagues accomplished just that, using terahertz (one trillion cycles per second) laser light spectroscopy to examine and nudge these materials into revealing the symmetry switching mechanisms of their properties.

In this experiment, the team altered the symmetry of the electronic structure of the material, using laser pulses to twist the lattice arrangement of the crystal. This light switch enables “Weyl points” in the material, causing electrons to behave as massless particles that can carry the protected, low dissipation current that is sought after.

“We achieved this giant dissipationless current by driving periodic motions of atoms around their equilibrium position in order to break crystal inversion symmetry,” says Ilias Perakis, professor of physics and chair at the University of Alabama at Birmingham. “This light-induced Weyl semimetal transport and topology control principle appears to be universal and will be very useful in the development of future quantum computing and electronics with high speed and low energy consumption.”

“What we’ve lacked until now is a low energy and fast switch to induce and control symmetry of these materials,” said Qiang Li, Group leader of the Brookhaven National Laboratory’s Advanced Energy Materials Group. “Our discovery of a light symmetry switch opens a fascinating opportunity to carry dissipationless electron current, a topologically protected state that doesn’t weaken or slow down when it bumps into imperfections and impurities in the material.”

The research is further discussed in the paper “A Light-induced Phononic Symmetry Switch and Giant Dissipationless Topological Photocurrent in ZrTe5,” authored by L. Luo, D. Cheng, B. Song, L.-L. Wang, C. Vaswani, P. M. Lozano, G. Gu, C. Huang, R. H. J. Kim, Z. Liu, J.-M. Park, Y. Yao, K.-M. Ho, I. E. Perakis, Q. Li and J. Wang; and published in Nature Materials.

Terahertz photocurrent and laser spectroscopy experiments and model building were performed at Ames Laboratory. Sample development and magneto-transport measurements were conducted by Brookhaven National Laboratory. Data analysis was conducted by the University of Alabama at Birmingham. First-principles calculations and topological analysis were conducted by the Center for the Advancement of Topological Semimetals, an Energy Frontier Research Center funded by the DOE Office of Science.

Reference: Luo, L., Cheng, D., Song, B. et al. A light-induced phononic symmetry switch and giant dissipationless topological photocurrent in ZrTe5. Nat. Mater. (2021). https://doi.org/10.1038/s41563-020-00882-4

Provided by AMES Laboratory

About AMES Laboratory

Ames Laboratory is a U.S. Department of Energy Office of Science National Laboratory operated by Iowa State University. Ames Laboratory creates innovative materials, technologies and energy solutions. We use our expertise, unique capabilities and interdisciplinary collaborations to solve global problems.

Ames Laboratory is supported by the Office of Science of the U.S. Department of Energy. The Office of Science is the single largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit https://energy.gov/science.

New Clues Help Explain Why PFAS Chemicals Resist Remediation (Chemistry)

Work Suggests New Avenues for Cleaning Up These ‘Forever Chemicals’

The synthetic chemicals known as PFAS, short for perfluoroalkyl and polyfluoroalkyl substances, are found in soil and groundwater where they have accumulated, posing risks to human health ranging from respiratory problems to cancer.

Research led by Konstantinos Kostarelos of UH Energy suggests why PFAS, known as “forever chemicals” because they can persist in the environment for decades, are so difficult to permanently remove and offers new avenues for better remediation practices.

New research from the University of Houston and Oregon State University published in Environmental Science and Technology Letters suggests why these “forever chemicals” – so called because they can persist in the environment for decades – are so difficult to permanently remove and offers new avenues for better remediation practices.

The work focused on the interactions sparked when firefighters use firefighting foam, which contains PFAS, to combat fires involving jet fuel, diesel or other hydrocarbon-based fuels. Firefighter training sites are well-documented sources of PFAS pollution.   

Konstantinos Kostarelos, a researcher with UH Energy and corresponding author for the work, said the interactions form a viscous water-in-oil microemulsion, which chemical analysis determined retains a high level of the PFAS.

Unlike many emulsions of oil and liquid, which separate into their component parts over time, these microemulsions – comprised of liquids from the firefighting foam and the hydrocarbon-based fuel – retain their composition, Kostarelos said. “It behaves like a separate phase: the water phase, oil phase and the microemulsion phase. And the microemulsion phase encapsulates these PFAS.”

Experimental trials that simulate the subsurface determined about 80% of PFAS were retained in the microemulsions when they flow through the soil, he said. “If they passed through easily, they wouldn’t have been so persistent over the course of decades.”

Produced during the post-World War II chemical boom, PFAS are found in consumer products ranging from anti-stain treatments to Teflon and microwave popcorn bags, in addition to firefighting foam. They were prized because they resist heat, oil and water – traditional methods of removing or breaking down chemicals – as a result of the strong bond between the carbon and fluorine atoms that make up PFAS molecules.

They have been the target of lawsuits and regulatory actions, and new chemical formulations have shortened their half-life.

In the meantime, the toxic legacy of the older formulations continues to resist permanent remediation. Kostarelos said the new understanding of microemulsion formation will help investigators better identify the source of the contamination, as well as stimulate new methods for clean-up efforts.

“It’s very viscous,” he said. “That’s very useful information for designing a way to recover the microemulsion.”

The project was funded by the Strategic Environmental Research and Development Program of the U.S. Department of Defense. In addition to Kostarelos, co-authors on the publication include Pushpesh Sharma of UH; and Emerson Christie, Thomas Wanzek and Jennifer Field, all of Oregon State University.

Reference: Konstantinos Kostarelos, Pushpesh Sharma, Emerson Christie, Thomas Wanzek, and Jennifer Field, “Viscous Microemulsions of Aqueous Film-Forming Foam (AFFF) and Jet Fuel A Inhibit Infiltration and Subsurface Transport”, Environ. Sci. Technol. Lett. 2020. https://pubs.acs.org/doi/10.1021/acs.estlett.0c00868?ref=pdf
https://doi.org/10.1021/acs.estlett.0c00868

Provided by University of Houston

Fatty Acid May Help Combat Multiple Sclerosis (Medicine)

The abnormal immune system response that causes multiple sclerosis (MS) by attacking and damaging the central nervous system can be triggered by the lack of a specific fatty acid in fat tissue, according to a new Yale study. The finding suggests that dietary change might help treat some people with the autoimmune disease.

The study was published Jan. 19 in The Journal of Clinical Investigation.

Graphical abstract by Pompura et al.

Fat tissue in patients diagnosed with MS lack normal levels of oleic acid, a monounsaturated fatty acid found at high levels in, for instance, cooking oils, meats (beef, chicken, and pork), cheese, nuts, sunflower seeds, eggs, pasta, milk, olives, and avocados, according to the study.

This lack of oleic acids leads to a loss of the metabolic sensors that activate T cells, that mediate the immune system’s response to infectious disease, the Yale team found. Without the suppressing effects of these regulatory T cells, the immune system can attack healthy central nervous system cells and cause the vision loss, pain, lack of coordination and other debilitating symptoms of MS.

When researchers introduced oleic acids into the fatty tissue of MS patients in laboratory experiments, levels of regulatory T cells increased, they found.

“We’ve known for a while that both genetics and the environment play a role in the development of MS,” said senior author David Hafler, William S. and Lois Stiles Edgerly Professor of Neurology and professor of immunobiology and chair of the Department of Neurology. “This paper suggests that one of environmental factors involved is diet.”

Hafler noted that obesity triggers unhealthy levels of inflammation and is a known risk factor for MS, an observation that led him to study the role of diet in MS.

He stressed, however, that more study is necessary to determine whether eating a diet high in oleic acid can help some MS patients.

Reference: Saige L. Pompura, Allon Wagner, Alexandra Kitz, Nir Yosef et al., “Oleic acid restores suppressive defects in tissue-resident FOXP3 Tregs from patients with multiple sclerosis”, J Clin Invest. 2021;131(2):e138519. https://doi.org/10.1172/JCI138519. https://www.jci.org/articles/view/138519

Provided by Yale University

How To Train A Robot (Using AI and Computers)? (Computer Science)

UT Arlington computer scientists use TACC systems to generate synthetic objects for robot training.

Before he joined the University of Texas at Arlington as an Assistant Professor in the Department of Computer Science and Engineering and founded the Robotic Vision Laboratory there, William Beksi interned at iRobot, the world’s largest producer of consumer robots (mainly through its Roomba robotic vacuum).

Examples of 3D point clouds synthesized by the progressive conditional generative adversarial network (PCGAN) for an assortment of object classes. PCGAN generates both geometry and color for point clouds, without supervision, through a coarse to fine training process. [Credit: William Beksi, Mohammad Samiul Arshad, UT Arlington]

To navigate built environments, robots must be able to sense and make decisions about how to interact with their locale. Researchers at the company were interested in using machine and deep learning to train their robots to learn about objects, but doing so requires a large dataset of images. While there are millions of photos and videos of rooms, none were shot from the vantage point of a robotic vacuum. Efforts to train using images with human-centric perspectives failed.

Beksi’s research focuses on robotics, computer vision, and cyber-physical systems. “In particular, I’m interested in developing algorithms that enable machines to learn from their interactions with the physical world and autonomously acquire skills necessary to execute high-level tasks,” he said.

Years later, now with a research group including six PhD computer science students, Beksi recalled the Roomba training problem and begin exploring solutions. A manual approach, used by some, involves using an expensive 360 degree camera to capture environments (including rented Airbnb houses) and custom software to stitch the images back into a whole. But Beksi believed the manual capture method would be too slow to succeed.

Instead, he looked to a form of deep learning known as generative adversarial networks, or GANs, where two neural networks contest with each other in a game until the ‘generator’ of new data can fool a ‘discriminator.’ Once trained, such a network would enable the creation of an infinite number of possible rooms or outdoor environments, with different kinds of chairs or tables or vehicles with slightly different forms, but still — to a person and a robot — identifiable objects with recognizable dimensions and characteristics.

“You can perturb these objects, move them into new positions, use different lights, color and texture, and then render them into a training image that could be used in dataset,” he explained. “This approach would potentially provide limitless data to train a robot on.”

Examples of 3D point clouds synthesized by PCGAN. [Credit: William Beksi, Mohammad Samiul Arshad, UT Arlington]

“Manually designing these objects would take a huge amount of resources and hours of human labor while, if trained properly, the generative networks can make them in seconds,” said Mohammad Samiul Arshad, a graduate student in Beksi’s group involved in the research.

GENERATING OBJECTS FOR SYNTHETIC SCENES

After some initial attempts, Beksi realized his dream of creating photorealistic full scenes was presently out of reach. “We took a step back and looked at current research to determine how to start at a smaller scale – generating simple objects in environments.”

Beksi and Arshad presented PCGAN, the first conditional generative adversarial network to generate dense colored point clouds in an unsupervised mode, at the International Conference on 3D Vision (3DV) in Nov. 2020. Their paper, “A Progressive Conditional Generative Adversarial Network for Generating Dense and Colored 3D Point Clouds,” shows their network is capable of learning from a training set (derived from ShapeNetCore, a CAD model database) and mimicking a 3D data distribution to produce colored point clouds with fine details at multiple resolutions.

“There was some work that could generate synthetic objects from these CAD model datasets,” he said. “But no one could yet handle color.”

In order to test their method on a diversity of shapes, Beksi’s team chose chairs, tables, sofas, airplanes, and motorcycles for their experiment. The tool allows the researchers to access the near-infinite number of possible versions of the set of objects the deep learning system generates.

“Our model first learns the basic structure of an object at low resolutions and gradually builds up towards high-level details,” he explained. “The relationship between the object parts and their colors — for examples, the legs of the chair/table are the same color while seat/top are contrasting — is also learned by the network. We’re starting small, working with objects, and building to a hierarchy to do full synthetic scene generation that would be extremely useful for robotics.”

They generated 5,000 random samples for each class and performed an evaluation using a number of different methods. They evaluated both point cloud geometry and color using a variety of common metrics in the field. Their results showed that PCGAN is capable of synthesizing high-quality point clouds for a disparate array of object classes.

SIM2REAL

Another issue that Beksi is working on is known colloquially as ‘sim2real.’ “You have real training data, and synthetic training data, and there can be subtle differences in how an AI system or robot learns from them,” he said. “‘Sim2real’ looks at how to quantify those differences and make simulations more realistic by capturing the physics of that scene – friction, collisions, gravity — and by using ray or photon tracing.”

The next step for Beksi’s team is to deploy the software on a robot, and see how it works in relationship to the sim-to-real domain gap.

The training of the PCGAN model was made possible by TACC’s Maverick 2 deep learning resource, which Beksi and his students were able to access through the University of Texas Cyberinfrastructure Research (UTRC) program, which provides computing resources to researchers at any of the UT System’s 14 institutions.

“If you want to increase resolution to include more points and more detail, that increase comes with an increase in computational cost,” he noted. “We don’t have those hardware resources in my lab, so it was essential to make use of TACC to do that.”

In addition to computation needs, Beksi required extensive storage for the research. “These datasets are huge, especially the 3D point clouds,” he said. “We generate hundreds of megabytes of data per second; each point cloud is around 1 million points. You need an enormous amount of storage for that.”

While Beksi says the field is still a long way from having really good robust robots that can be autonomous for long periods of time, doing so would benefit multiple domains, including health care, manufacturing, and agriculture.

“The publication is just one small step toward the ultimate goal of generating synthetic scenes of indoor environments for advancing robotic perception capabilities,” he said.

Provided by TACC

Light-controlled Higgs Modes Found in Superconductors; Potential Sensor, Computing Uses (Physics)

Iowa State’s Jigang Wang and a team of researchers have discovered a short-lived form of the famous Higgs boson — subject of a groundbreaking search at the Large Hadron Collider — within an iron-based superconductor. This Higgs mode can be accessed and controlled by laser light flashing on the superconductor at trillions of pulses per second.

Even if you weren’t a physics major, you’ve probably heard something about the Higgs boson.

There was the title of a 1993 book by Nobel laureate Leon Lederman that dubbed the Higgs “The God Particle.” There was the search for the Higgs particle that launched after 2009’s first collisions inside the Large Hadron Collider in Europe. There was the 2013 announcement that Peter Higgs and Francois Englert won the Nobel Prize in Physics for independently theorizing in 1964 that a fundamental particle – the Higgs – is the source of mass in subatomic particles, making the universe as we know it possible.

This illustration shows light at trillions of pulses per second (red flash) accessing and controlling Higgs modes (gold balls) in an iron-based superconductor. Even at different energy bands, the Higgs modes interact with each other (white smoke). Illustration courtesy of Jigang Wang.

(Plus, there are the Iowa State University physicists on the author list of a 2012 research paper describing how the ATLAS Experiment at the collider observed a new particle later confirmed to be the Higgs.)

And now Jigang Wang, a professor of physics and astronomy at Iowa State and a senior scientist at the U.S. Department of Energy’s Ames Laboratory, and a team of researchers have discovered a form of the famous particle within a superconductor, a material capable of conducting electricity without resistance, generally at very cold temperatures. 

Wang and his collaborators – including Chang-Beom Eom, the Raymond R. Holton Chair for Engineering and Theodore H. Geballe Professor at the University of Wisconsin-Madison; Ilias Perakis, professor and chair of physics at the University of Alabama at Birmingham; and Eric Hellstrom, professor and interim chair of mechanical engineering at Florida State University – report the details in a paper recently published online by the journal Nature Communications.

They write that in lab experiments they’ve found a short-lived “Higgs mode” within iron-based, high-temperature (but still very cold), multi-energy band, unconventional superconductors.

A quantum discovery

This Higgs mode is a state of matter found at the quantum scale of atoms, their electronic states and energetic excitations. The mode can be accessed and controlled by laser light flashing on the superconductor at terahertz frequencies of trillions of pulses per second. The Higgs modes can be created within different energy bands and still interact with each other.

Wang said this Higgs mode within a superconductor could potentially be used to develop new quantum sensors.

“It’s just like the Large Hadron Collider can use the Higgs particle to detect dark energy or antimatter to help us understand the origin of the universe,” Wang said. “And our Higgs mode sensors on the table-top have the potential help us discover the hidden secrets of quantum states of matter.”

That understanding, Wang said, could advance a new “quantum revolution” for high-speed computing and information technologies.

“It’s one way this exotic, strange, quantum world can be applied to real life,” Wang said.

Light control of superconductors

The project takes a three-pronged approach to accessing and understanding the special properties, such as this Higgs mode, hidden within superconductors:

Wang’s research group uses a tool called quantum terahertz spectroscopy to visualize and steer pairs of electrons moving through a superconductor. The tool uses laser flashes as a control knob to accelerate supercurrents and access new and potentially useful quantum states of matter.

Eom’s group developed the synthesis technique that produces crystalline thin films of the iron-based superconductor with high enough quality to reveal the Higgs mode. Hellstrom’s group developed deposition sources for the iron-based superconducting thin film development.

Perakis’ group led the development of quantum models and theories to explain the results of the experiments and to simulate the salient features that come from the Higgs mode.

The work has been supported by a grant to Wang from the National Science Foundation and grants to Eom and Perakis from the U.S. Department of Energy.

“Interdisciplinary science is the key here,” Perakis said. “We have quantum physics, materials science and engineering, condensed matter physics, lasers and photonics with inspirations from fundamental, high-energy and particle physics.”

There are good, practical reasons for researchers in all those fields to work together on the project. In this case, students from the four research groups worked together with their advisors to accomplish this discovery.

“Scientists and engineers,” Wang wrote in a research summary, “have recently come to realize that certain materials, such as superconductors, have properties that can be exploited for applications in quantum information and energy science, e.g., processing, recording, storage and communication.”

Reference: Vaswani, C., Kang, J.H., Mootz, M. et al. Light quantum control of persisting Higgs modes in iron-based superconductors. Nat Commun 12, 258 (2021). https://www.nature.com/articles/s41467-020-20350-6 https://doi.org/10.1038/s41467-020-20350-6

Provided by Iowa State University