Culture

Teaching physics to neural networks removes 'chaos blindness'

Researchers from North Carolina State University have discovered that teaching physics to neural networks enables those networks to better adapt to chaos within their environment. The work has implications for improved artificial intelligence (AI) applications ranging from medical diagnostics to automated drone piloting.

Neural networks are an advanced type of AI loosely based on the way that our brains work. Our natural neurons exchange electrical impulses according to the strengths of their connections. Artificial neural networks mimic this behavior by adjusting numerical weights and biases during training sessions to minimize the difference between their actual and desired outputs. For example, a neural network can be trained to identify photos of dogs by sifting through a large number of photos, making a guess about whether the photo is of a dog, seeing how far off it is and then adjusting its weights and biases until they are closer to reality.

The drawback to this neural network training is something called "chaos blindness" - an inability to predict or respond to chaos in a system. Conventional AI is chaos blind. But researchers from NC State's Nonlinear Artificial Intelligence Laboratory (NAIL) have found that incorporating a Hamiltonian function into neural networks better enables them to "see" chaos within a system and adapt accordingly.

Simply put, the Hamiltonian embodies the complete information about a dynamic physical system - the total amount of all the energies present, kinetic and potential. Picture a swinging pendulum, moving back and forth in space over time. Now look at a snapshot of that pendulum. The snapshot cannot tell you where that pendulum is in its arc or where it is going next. Conventional neural networks operate from a snapshot of the pendulum. Neural networks familiar with the Hamiltonian flow understand the entirety of the pendulum's movement - where it is, where it will or could be, and the energies involved in its movement.

In a proof-of-concept project, the NAIL team incorporated Hamiltonian structure into neural networks, then applied them to a known model of stellar and molecular dynamics called the Hénon-Heiles model. The Hamiltonian neural network accurately predicted the dynamics of the system, even as it moved between order and chaos.

"The Hamiltonian is really the 'special sauce' that gives neural networks the ability to learn order and chaos," says John Lindner, visiting researcher at NAIL, professor of physics at The College of Wooster and corresponding author of a paper describing the work. "With the Hamiltonian, the neural network understands underlying dynamics in a way that a conventional network cannot. This is a first step toward physics-savvy neural networks that could help us solve hard problems."

The work appears in Physical Review E and is supported in part by the Office of Naval Research (grant N00014-16-1-3066). NC State postdoctoral researcher Anshul Choudhary is first author. Bill Ditto, professor of physics at NC State, is director of NAIL. Visiting researcher Scott Miller; Sudeshna Sinha, from the Indian Institute of Science Education and Research Mohali; and NC State graduate student Elliott Holliday also contributed to the work.

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North Carolina State University

Environmental conditions found to affect stability of virus that causes COVID-19

HUNTINGTON, W.Va. - A new study led by Marshall University researcher M. Jeremiah Matson found that environmental conditions affect the stability of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in human nasal mucus and sputum.

Matson, the lead author on a study published earlier this month as an early release in Emerging Infectious Diseases, the journal of the Centers for Disease Control and Prevention (CDC), is a student in the combined Doctor of Medicine and Doctor of Philosophy in Biomedical Research program at the Marshall University Joan C. Edwards School of Medicine.

SARS-CoV-2, the virus that causes the disease known as COVID-19, was found to be less stable at higher humidity and warmer temperatures. In the study, SARS-CoV-2 was mixed with human nasal mucus and sputum specimens, which were then exposed to three different sets of temperature and humidity for up to seven days. Samples were collected throughout the study and analyzed for the presence of infectious virus as well as viral RNA alone, which is not infectious. Viral RNA was consistently detectable throughout the seven-day study, while infectious virus was detectable for up to approximately 12-48 hours, depending on the environmental conditions.

"The COVID-19 pandemic has been a sobering reminder that infectious diseases continue to be a major public health threat and require sustained research commitment," Matson said. "While this is a small study that only addresses the potential for fomite [an object that may be contaminated with infectious agents] transmission, which is thought to be less important than droplet transmission for SARS-CoV-2, it nevertheless is informative for public health risk assessment."

In a second study, also released this month in Emerging Infectious Diseases, Matson was part of a team of researchers that evaluated the effectiveness of N95 respirator decontamination and reuse against SARS-CoV-2. Vaporized hydrogen peroxide and ultraviolet light were found to be most effective if proper fit and seal were maintained.

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Marshall University Joan C. Edwards School of Medicine

COVID-19 news from Annals of Internal Medicine

Below please find a summary and link(s) of new coronavirus-related content published today in Annals of Internal Medicine. The summary below is not intended to substitute for the full article as a source of information. A collection of coronavirus-related content is free to the public at http://go.annals.org/coronavirus.

ACP Proposes Policies and Action to Confront Systemic Racism, Discrimination and Injustices in Health and Law Enforcement

ACP Commits to Being an Anti-Racist Organization, Says Racism Is a Public Health Issue

@acpinternists, @annalsofim

The American College of Physicians (ACP) believes there is an urgent need to speak out on the ongoing racism and violence that are regularly directed at Black individuals and other people of color in the United States, including racism and violence committed by law enforcement, and that ongoing racism continues to be an urgent public health issue requiring systemic change. In a new policy paper published today, ACP condemns the injustices and harms experienced by Black individuals and other people of color as a result of racism and details the ways that pervasive systemic racism, discrimination, and violence throughout society have adverse individual and community health consequences. ACP reaffirms and commits to expanding on its previous policies to confront racial and ethnic disparities, discrimination and racism in health, and offers new recommendations to address racism in law enforcement and its impact on public health.

ACP's new policy is supported by an extensive review of the evidence of how racism and discrimination in health care and in law enforcement, are public health issues. The policy offers specific ideas "as a starting point" to address institutional discrimination, racism and bias in law enforcement, an issue that ACP has not previously addressed in policy papers and advocacy. The positions offer suggested solutions to increase transparency and accountability, and to adopt best practices that encourage safer law enforcement practices and reduce violent interactions with civilians. Read the full text: https://www.acpjournals.org/doi/10.7326/M20-4195.

Media contacts: A PDF for this article is not yet available. Please click the link to read full text. To speak with someone from ACP, please contact Jacquelyn Blaser at jblaser@acponline.org.

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American College of Physicians

New adjuvant successful in extending immunity against HIV

ATLANTA - Researchers at the Yerkes National Primate Research Center and the Emory Vaccine Center (EVC) are first to show a new adjuvant, 3M-052, helps induce long-lasting immunity against HIV. The study results are published today in Science Immunology.

In this pre-clinical study that included 90 rhesus monkeys, the researchers showed 3M-052, a new, synthetic small molecule that targets a specific receptor (TLR 7/8), successfully induced vaccine-specific, long-lived bone marrow plasma cells (BM-LLPCs), which are critical for durable immunity. In a striking observation, 3M-052-induced BM-LLPCs were maintained at high numbers for more than one year after vaccination. This prolonged interval is not only feasible in monitoring pre-clinical effectiveness, it is also highly informative in down selecting vaccine candidates.

First author Sudhir Pai Kasturi, PhD, an assistant professor in the Department of Pathology and Laboratory Medicine and a research assistant professor at Yerkes and the EVC, says, "We have known adjuvants are critical immunity-boosting supplements that help improve the effectiveness of vaccines. Until now, however, it has been unclear which class of adjuvants can promote stable and long-lived immunity in nonhuman primate models. Our study provides that information."

Co-senior author Rafi Ahmed, PhD, director of the Emory Vaccine Center, adds, "The key to a successful vaccine is durability of immune responses. Antibodies provide the first line of defense against pathogens, and antibody levels are maintained by the generation of long-lived plasma cells that reside in bone marrow. Our study identifies an adjuvant that is effective in generating such long-lived plasma cells in bone marrow. This finding has implications for developing successful vaccines against HIV, influenza and, especially important now, COVID-19.

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Emory Health Sciences

SARS-CoV-2 transmission to animals: Monitoring needed to mitigate risk

As evidence mounts for the possibility of SARS-CoV-2 infecting various animals, scientists at UCL say a global effort is needed to reduce the risk of the virus later returning to people.

In a comment piece for The Lancet Microbe, researchers write that if the virus becomes common in an animal population that lives near people, such as pets or livestock, there would be a risk that another outbreak could occur even if the virus is eradicated in people in the area.

The authors call for more research into which animals are susceptible to SARS-CoV-2, the virus causing the Covid-19 disease, and suggest implementing surveillance programmes to regularly test animals that could pose the highest risks of transmission.

Co-author Professor Joanne Santini (UCL Structural & Molecular Biology) said: "There is increasing evidence that some animals can catch SARS-CoV-2 from people, and might subsequently transmit it to other people - but we don't know just how much of a risk this is, as it's an area of study that has not yet been prioritised.

"We need to develop surveillance strategies to ensure we don't get taken by surprise by a large outbreak in animals, which could pose a threat not just to animal health but to human health as well.

"Virus transmission in animal populations could become irreversible if left unchecked, and may threaten the success of existing public health measures if people continue to catch the virus from an infected population of animals."

The authors write that the immense scale of the Covid-19 pandemic compounds the possibility of sufficient animals becoming 'reservoirs' of the virus, which could be more likely than for past epidemics, such as the more contained SARS-CoV-1 outbreak in 2002-2003.

Professor Santini and co-author Professor Sarah Edwards (UCL Science & Technology Studies) reviewed evidence from case studies, experiments testing infection in small groups of animals, as well as laboratory and modelling studies describing likely infection mechanisms.

Modelling and lab studies suggest that SARS-CoV-2 could in theory be transmitted to numerous animals, based on findings that the spike protein on the virus attaches to host cells, using a protein that is found in many different species.

The research paper advises that, once scientists identify which animals could become infected, they then need to figure out whether they will become unwell or remain asymptomatic, and whether an infected individual is able to then transmit the virus to other animals or even to humans.

Notably, there have been recent cases in the Netherlands of farmed mink becoming infected with SARS-CoV-2, leading to two people catching the virus from these animals, in an outbreak that has led to thousands of mink being culled. The researchers say this example highlights not only the risk to human health, but also animal welfare concerns and potential loss of livelihoods in the agricultural sector.

Professor Edwards commented: "There's an urgent need for widespread surveillance, by testing samples, preferably non-invasively, from large numbers of animals, particularly pets, livestock and wildlife that are in close proximity to human populations. More laboratory experiments on small numbers of animals are unlikely to give us the evidence needed to be confident that certain species are entirely safe, making major surveillance work the only real option here.

"We need more information, at the same time as taking simple precautionary measures especially with species which have the potential to spread the virus rapidly in the wild. A robust risk assessment would also require reviewing our ability to manage an outbreak in those animals, namely our ability to isolate, protect, or contain different animals."

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University College London

High cortisol levels associated with greater risk of death from COVID-19

COVID-19 patients with extremely high levels of the stress hormone cortisol in their blood are more likely to deteriorate quickly and die, according to new research published today.

The study, led by NIHR Research Professor Waljit Dhillo from Imperial College London and Consultant Endocrinologist at Imperial College Healthcare NHS Trust, provides the first data to show that cortisol levels are a marker of the severity of the illness. The researchers suggest they can be used to identify those patients who are more likely to need intensive care.

Cortisol is produced by the body in response to stress such as illness, triggering changes in metabolism, heart function and the immune system to help our bodies cope. Our cortisol levels when healthy and resting are 100-200 nm/L and nearly zero when we sleep.

When ill patients have low levels of cortisol, it can be life threatening. Excessive levels of cortisol during illness can be equally dangerous, leading to increased risk of infection and poor outcomes. In the new observational study of 535 patients, of whom 403 were confirmed to have COVID-19, cortisol levels in patients with COVID-19 were significantly higher than in those without. The levels in the COVID-19 group ranged as high as 3241 - considerably higher even than after major surgery, when levels can top 1000.

Amongst the COVID-19 patients, those with a baseline cortisol level of 744 or less survived on average for 36 days. Patients with levels over 744 had an average survival of just 15 days.

Professor Dhillo, Head of Division of Diabetes, Endocrinology and Metabolism at Imperial College London, said: "From an endocrinologist's perspective, it makes sense that those COVID-19 patients who are the sickest will have higher levels of cortisol, but these levels are worryingly high.

"Three months ago when we started seeing this wave of COVID-19 patients here in London hospitals, we had very little information about how to best triage people. Now, when people arrive at hospital, we potentially have another simple marker to use alongside oxygen saturation levels to help us identify which patients need to be admitted immediately, and which may not. Having an early indicator of which patients may deteriorate more quickly will help us with providing the best level of care as quickly as possible, as well as helping manage the pressure on the NHS. In addition, we can also take cortisol levels into account when we are working out how best to treat our patients."

The study, published in The Lancet Diabetes & Endocrinology and funded by the National Institute for Health Research (NIHR) and the Medical Research Council, involved 535 patients admitted to three London hospitals - Charing Cross, Hammersmith and St Mary's - with suspected COVID-19 between 09 March and 22 April 2020. A COVID-19 swab test and routine blood tests - including a baseline measurement of cortisol levels - were performed within 48hrs of admission.

Over the study period, just under 27 per cent of the COVID-19 group died during the study period compared to just under 7per cent of the non-COVID-19 group.

Professor Dhillo and his team hope that their findings can now be validated in a larger scale clinical study.

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Imperial College London

Simple oral health steps help improve elite athletes' performance

Elite athletes who adopted simple oral health measures, such as using high fluoride toothpaste and cleaning between their teeth, reported significantly reduced negative effects on performance related to poor oral health, finds a study led by UCL.

The new research, published in BMJ Open Sport & Exercise Medicine, is the latest in a series of studies* led by the UCL Centre for Oral Health and Performance (COHP), based at UCL Eastman Dental Institute, which have found that elite athletes have substantial rates of oral disease**, including tooth decay and gum inflammation, and these symptoms negatively affected their wellbeing and sporting performance.

To help address this, researchers at UCL COHP designed a behavioural change programme aimed at better educating elite athletes about oral health and providing some simple interventions to improve their daily oral health routines.

Explaining the study, lead author, Dr Julie Gallagher (UCL Eastman Dental Institute), said: "Poor oral health of elite athletes is common and is associated with negative performance. However, compared with other health and training pressures, oral health care is not a high priority in elite sport.

"We therefore wanted to develop a programme which was aligned with the existing high-performance culture of the athletes and their teams. Underpinning the study was health behaviour psychology, which included education, self-motivation, goal setting, and an easy to use toolkit, ensuring the athletes had a readily available opportunity to improve."

In total, 62 athletes from two Great Britain Olympic Teams, rowing and cycling, and one Premiership Rugby Club, Gloucester Rugby, were recruited to the study.

Athletes and support teams were asked to watch a 10-minute presentation which focussed on building motivation to improve oral health, and three 90-second information films, featuring GB rower Zak Lee-Green, which focussed on increasing oral health knowledge and skills to perform optimum oral health behaviour.

In addition, each athlete received an oral health screening to check for diseases such as caries (tooth decay) and gingivitis (gum inflammation). They were then given a bespoke follow up report with tailored advice and an oral health toolkit, containing a manual toothbrush, prescription fluoride toothpaste and flosspicks. As a minimum, they were also asked to brush their teeth for two minutes twice a day, to include brushing before training in the morning and before bed in the evening.

In total 89% of athletes completed the four-month study. On completion athletes were asked to fill in an oral health knowledge questionnaire, undergo a follow-up gingival (oral disease) assessment and evaluate the oral health kit.

Results

The study found that the behaviour change model was associated both with reductions in self-reported negative performance impacts and in improvements in oral health behaviours.

Athlete use of prescription strength fluoride toothpaste increased from 8 (12.9%) to 45 (80.4%), use of interdental cleaning aids at least two to three times per week increased from 10 (16.2%) to 21 (34%). Bleeding (gums) score remained unchanged. A desire to avoid inflammation in the body resulting from poor oral health was cited by 93% of athletes as the key motivator to make changes to their oral health routine. ]

Improvements in sporting performance were measured using the Oslo Sports Trauma Research Center Overuse Injury Questionnaire (OSTRC-O), developed to monitor illness and injury in elite athletes. UCL COHP adapted the questionnaire to focus on oral health, asking the extent to which the oral health problem affected 1) sports participation, 2) training volume; 3) sporting performance; and 4) the extent to which the individual has experienced oral pain.

As a result of the behavioural change programme the mean OSTRC score across athletes reduced from 8.73 (out of 100) to 2.73, which while low at the outset, does indicate a statistically significant reduction in problems associated with oral health and sporting performance.

In addition the number (proportion) of athletes who reported a 0 (zero) score, meaning they had no negative sporting impact from oral health conditions, increased from 32 (51.6%) at baseline to 54 (98.2%) at the end of the study

Dr Gallagher added: "Through our previous research and focus group sessions, we established that athletes' motivations for taking part in the study were both appearance and athletic performance, with many keen to avoid gum inflammation affecting other parts of their bodies, which can happen in serious cases.

"We believe that bringing behaviour change science together with an understanding of the athletes' and teams' priorities is key to making changes stick."
There are a number of reasons athletes are more likely to have poor oral health: physical activity causes a dry mouth, which in the long-term increases risk of tooth decay and gum diseases, along with frequent sugar intakes from normal diet and energy supplements.

Co-author and UCL Centre for Oral Health and Performance lead, Professor Ian Needleman, said: "To compete at the top level elite athletes need to make the most of marginal gains and maintaining good oral health has been proven to have real performance benefits.

"With so many other competing interests, such as training, nutrition, sleep and mental health, it is remarkable to see such great rates of adherence to the new routines in a high-performance environment."

Zak Lee-Green, a member of the GB Rowing Team and a dentist who took part in the study, said: "As athletes we are acutely aware of the marginal gains required to achieve peak performance and maintaining good oral health is a prime example of an area often overlooked.

"This programme has gone a step further than showing the positive effect of excellent oral health on everyday life and has shown the potential benefits for improved performance, helping us reach the highest levels of sport. It can only be a step in the right direction if the sporting role models of the present and future are managing their oral health in the same way that they do their elite training."

Dr Nigel Jones, Head of Medical Services at British Cycling, said: "The topic of oral health amongst athletes is an important one, especially as it can be linked to performance. My role with the Great Britain Cycling Team is to ensure the holistic well-being of our cyclists, and as oral health can have a big impact on immune function as well as being important in its own right, I wanted to support this project. The learnings which the riders took from the study have been invaluable and will be deployed across the whole team as we ramp up our preparations for the Tokyo Olympic and Paralympic Games next year."

This behavioural change study was based on the COM-B model, which identifies sources of behaviour that could provide opportunities for intervention.

Capability (C) that is, the person having the physical skills and knowledge to perform the behaviour, Opportunity (O), that is, access to the necessary materials and social environment such that the person feels able to undertake the new behaviour, while Motivation (M) refers to a person deciding to adopt the behaviour

Researchers believe the bespoke model they have developed could be used for other health promotion needs in elite sport.

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University College London

COVID-19 news from Annals of Internal Medicine

Below please find a summary and link(s) of new coronavirus-related content published today in Annals of Internal Medicine. The summary below is not intended to substitute for the full article as a source of information. A collection of coronavirus-related content is free to the public at http://go.annals.org/coronavirus.

1. Living Practice Points from ACP: Advice on Use of N95, Surgical, and Cloth Masks to Prevent COVID-19
@acpinternists, @annalsofim

The American College of Physicians (ACP) issued new Practice Points on the effectiveness of N95 respirators, surgical masks, and cloth masks for the prevention of COVID-19 disease in addition to standard precautions (such as hand washing, gloves, etc.) in both healthcare settings and community settings. In the health care setting, ACP says that healthcare personnel should wear N95 respirators when in close contact with suspected or known COVID-19 patients. ACP also says that all healthcare personnel, patients, and visitors who are not in close contact with patients with suspected or known COVID-19 should use surgical masks in healthcare settings to reduce the risk of transmission of SARS-CoV-2 infection. ACP says asymptomatic or symptomatic persons in community settings should follow community and statewide public health guidelines for mask use, which should take into account factors such as local demographics (e.g., high risk populations), epidemiologic data (e.g., reproduction rate, daily case counts, hospitalizations, and deaths), and exposure context (e.g., number of people, indoor vs outdoors, ventilation etc.). Read the full text: https://www.acpjournals.org/doi/10.7326/M20-3234.

Media contacts: A PDF for this article is not yet available. Please click the link to read full text. To speak with someone from ACP, please contact Andy Hachadorian at Ahachadorian@acponline.org.

2. White Coats for Black Lives: The Time Has Come for Action
@valstonemd, @BrighamWomens

The author from Brigham and Women's Hospital discusses actions academic medical centers and their leaders should take toward eradicating racism at their institutions. She stresses that transforming academic culture is essential to the care of black patients and to provide a robust community of support for black medical students, trainees, and faculty. Read the full text: https://www.acpjournals.org/doi/10.7326/M20-4280.

Media contacts: A PDF for this article is not yet available. Please click the link to read full text. The lead author, Valerie E. Stone, MD, MPH, can be contacted directly at vstone@bwh.harvard.edu.

3. COVID-19 Across Africa: Epidemiologic Heterogeneity and Necessity of Contextually Relevant Transmission Models and Intervention Strategies
@JohnsHopkinsSPH, @TwahirwaOlivier, @sdbaral

Authors from John Hopkins Bloomberg School of Public Health discuss the COVID-19 pandemic on the African continent. The authors describe why the international community should be hesitant in developing forecasts and prevention strategies for COVID-19 in the absence of integration of African data. Input from leadership of African institutions should be considered, as they have a long history of effective measures to mitigate infectious diseases, such as Ebola, Zika, malaria, and dengue, among others. Read the full text: https://www.acpjournals.org/doi/10.7326/M20-2628.

Media contacts: A PDF for this article is not yet available. Please click the link to read full text. The lead author, Jean Olivier Twahirwa Rwema, MD, MPH, can be reached directly at jtwahir1@jhu.edu.

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American College of Physicians

The Parkinson's disease gut has an overabundance of opportunistic pathogens

image: Haydeh Payami

Image: 
UAB

BIRMINGHAM, Ala. - Parkinson's disease is a common, progressive and debilitating neurodegenerative disease. It currently cannot be prevented or cured.

In 2003, Heiko Braak proposed that non-inherited forms of PD are caused by a pathogen in the gut. He hypothesized that the pathogen could pass through the intestinal mucosal barrier and spread to the brain through the nervous system. Up to now, there has been no evidence of a specific pathogen that may trigger PD.

Now Haydeh Payami, Ph.D., professor of neurology at the University of Alabama at Birmingham, and colleagues report for the first time a significant overabundance of a cluster of opportunistic pathogens in the guts of persons with PD, compared to control subjects.

"The exciting question is whether these are Braak's pathogens capable of triggering PD, or are they irrelevant to PD but able to penetrate the gut and grow, because the gut lining is compromised in PD," Payami said. "We emphasize that no claims can be made on function based solely on association. The identity of these microorganisms will enable experimental studies to determine whether and how they play a role in PD."

Payami and colleagues at UAB, Emory University, Albany Medical College and the University of Washington were able to identify these microorganisms because they performed the largest microbiome-wide association study of persons with PD and controls to date. Many previous studies have found altered gut microbiomes in persons with PD but did not detect an increase in opportunistic pathogens. Opportunistic pathogens are often harmless, but they can grow and cause infections if the immune system is compromised or if they penetrate into sterile sites of the body.

"We suspect the reason we were able to detect these microorganisms is that they are rare and we had a much larger sample size and power than prior studies," Payami said. Her researchers re-analyzed their 2017 study that had 197 cases and 130 controls, using a more advanced bioinformatics pipeline. They also analyzed a new, independent dataset with 323 cases of PD and 184 controls, in parallel to the first dataset. This allowed internal replication and the power to detect both rare and common signals. Previous PD microbiome studies have ranged from 10 to 197 PD cases and 10 to 130 controls.

A microbiome-wide association study uses advances in DNA sequencing and computational tools to look for microbial communities that may be associated with disease. There is emerging understanding that the gut microbiome -- which includes 500 to 1,000 bacterial species that have a mainly beneficial influence -- plays an important role in human health and disease.

Payami and colleagues also used hypothesis-free correlation network analysis to identify communities of co-occurring microorganisms. Network analysis is an important new tool in biology. An easily understood example of networks is a social network like Facebook, where one can map the connections between followers or friends. A few people will have a huge number of connections, some will have many, and a vast majority will have much fewer. A map of these connections is akin to an airline route map.

Using network analysis, Payami and colleagues found three polymicrobial clusters, and also found that each cluster shared functional characteristics. The first cluster was that of opportunistic pathogens overabundant in PD cases, a novel finding.

The other two clusters were confirmatory of previous studies. In comparison to controls, persons with PD had reduced levels of a cluster of microbes that produce short-chain fatty acids. In the third cluster, the persons with PD had elevated levels of two genera that are carbohydrate-metabolizing probiotic microbes.

Payami says the current study had a precise focus and an intentionally strict analytic execution. The rigor of the study included showing that the altered gut microbiomes in the PD cases were independent of sex, age, BMI, constipation, gastrointestinal discomfort, geography and diet. The 15 PD-associated genera that achieved microbiome-wide significance in both datasets were identified using two methods, and with or without covariate adjustment.

"There is more to be learned," Payami said, "with larger sample sizes with greater power, longitudinal studies to track change from prodromal to advanced disease, and by next-generation metagenome sequencing to broaden the scope from bacteria and archaea to include viruses and fungi, and improve the resolution to strain and gene level."

Credit: 
University of Alabama at Birmingham

Mayo finds convalescent plasma safe for diverse patients with COVID-19

ROCHESTER, Minn. - Mayo Clinic researchers and collaborators have found investigational convalescent plasma to be safe following transfusion in a diverse group of 20,000 patients. The findings -- from the U.S. Food and Drug Administration's Expanded Access Program for COVID-19 -- are reported in Mayo Clinic Proceedings.

The safety report assessed the seven days following transfusion for hospitalized patients between April 3 and June 11 who were deemed at risk of progressing to a severe or life-threatening condition. Nearly 40% of the patients were women; 20% African Americans; nearly 35% Hispanic and 5% Asian. Seven-day mortality rates declined to 8.6 % compared to 12% in a previous safety study of the first 5,000 transfused patients. Serious adverse events continued to be less than one percent.

"Our efforts to understand convalescent plasma continue," says Michael Joyner, M.D., principal investigator of the EAP at Mayo Clinic and lead author of the article. "We're optimistic but must remain objective as we assess increasing amounts of data."

This expanded safety report reveals a decline in mortality which appears contemporary with the more rapid availability of plasma for use, but the authors caution that this alone does not provide any evidence on effectiveness of convalescent plasma for treating COVID-19. Given the accelerating use of the therapy, research is now broadening its focus to determine indicators of efficacy. At this time, convalescent plasma therapy is the only antibody-based therapy for COVID-19.

"The 7000-plus physicians who are part of the program have done an exceptional job of offering convalescent plasma to a diverse group of patients, enrolling women as forty percent of the participants as well as significant numbers of patients who are of African American, Asian or Hispanic ethnicity," says researcher DeLisa Fairweather, Ph.D. "We hope recruitment of minority subjects continues to increase given the disproportionate burden these communities have faced with COVID-19."

The researchers say that while the mortality rate has decreased, the patients in the latter part of this study were less critically ill. They also say the decrease may be in part due to improved medical care based on increased knowledge during the pandemic and that more of the patients received the plasma earlier in their hospital treatment. They note that there was no system in place for delivering convalescent plasma in March and now there is sufficient donation to meet most of the demand. Also, as donors came forward more rapidly, it was more likely their plasma contained neutralizing antibodies.

Credit: 
Mayo Clinic

Are planets with oceans common in the galaxy? It's likely, NASA scientists find

image: This illustration shows NASA's Cassini spacecraft flying through plumes on Enceladus in October 2015.

Image: 
NASA/JPL-Caltech

Several years ago, planetary scientist Lynnae Quick began to wonder whether any of the more than 4,000 known exoplanets, or planets beyond our solar system, might resemble some of the watery moons around Jupiter and Saturn. Though some of these moons don't have atmospheres and are covered in ice, they are still among the top targets in NASA's search for life beyond Earth. Saturn's moon Enceladus and Jupiter's moon Europa, which scientists classify as "ocean worlds," are good examples.

"Plumes of water erupt from Europa and Enceladus, so we can tell that these bodies have subsurface oceans beneath their ice shells, and they have energy that drives the plumes, which are two requirements for life as we know it," says Quick, a NASA planetary scientist who specializes in volcanism and ocean worlds. "So if we're thinking about these places as being possibly habitable, maybe bigger versions of them in other planetary systems are habitable too."

Quick, of NASA's Goddard Space Flight Center in Greenbelt, Maryland, decided to explore whether -- hypothetically -- there are planets similar to Europa and Enceladus in the Milky Way galaxy. And, could they, too, be geologically active enough to shoot plumes through their surfaces that could one day be detected by telescopes.

Through a mathematical analysis of several dozen exoplanets, including planets in the nearby TRAPPIST-1 system, Quick and her colleagues learned something significant: More than a quarter of the exoplanets they studied could be ocean worlds, with a majority possibly harboring oceans beneath layers of surface ice, similar to Europa and Enceladus. Additionally, many of these planets could be releasing more energy than Europa and Enceladus.

Scientists may one day be able to test Quick's predictions by measuring the heat emitted from an exoplanet or by detecting volcanic or cryovolcanic (liquid or vapor instead of molten rock) eruptions in the wavelengths of light emitted by molecules in a planet's atmosphere. For now, scientists cannot see many exoplanets in any detail. Alas, they are too far away and too drowned out by the light of their stars. But by considering the only information available -- exoplanet sizes, masses and distances from their stars -- scientists like Quick and her colleagues can tap mathematical models and our understanding of the solar system to try to imagine the conditions that could be shaping exoplanets into livable worlds or not.

While the assumptions that go into these mathematical models are educated guesses, they can help scientists narrow the list of promising exoplanets to search for conditions favorable to life so that NASA's upcoming James Webb Space Telescope or other space missions can follow up.

"Future missions to look for signs of life beyond the solar system are focused on planets like ours that have a global biosphere that's so abundant it's changing the chemistry of the whole atmosphere," says Aki Roberge, a NASA Goddard astrophysicist who collaborated with Quick on this analysis. "But in the solar system, icy moons with oceans, which are far from the heat of the Sun, still have shown that they have the features we think are required for life."

To look for possible ocean worlds, Quick's team selected 53 exoplanets with sizes most similar to Earth, though they could have up to eight times more mass. Scientists assume planets of this size are more solid than gaseous and, thus, more likely to support liquid water on or below their surfaces. At least 30 more planets that fit these parameters have been discovered since Quick and her colleagues began their study in 2017, but they were not included in the analysis, which was published on June 18 in the journal Publications of the Astronomical Society of the Pacific.

With their Earth-size planets identified, Quick and her team sought to determine how much energy each one could be generating and releasing as heat. The team considered two primary sources of heat. The first, radiogenic heat, is generated over billions of years by the slow decay of radioactive materials in a planet's mantle and crust. That rate of decay depends on a planet's age and the mass of its mantle. Other scientists already had determined these relationships for Earth-size planets. So, Quick and her team applied the decay rate to their list of 53 planets, assuming each one is the same age as its star and that its mantle takes up the same proportion of the planet's volume as Earth's mantle does.

Next, the researchers calculated heat produced by something else: tidal force, which is energy generated from the gravitational tugging when one object orbits another. Planets in stretched out, or elliptical, orbits shift the distance between themselves and their stars as they circle them. This leads to changes in the gravitational force between the two objects and causes the planet to stretch, thereby generating heat. Eventually, the heat is lost to space through the surface.

One exit route for the heat is through volcanoes or cryovolcanoes. Another route is through tectonics, which is a geological process responsible for the movement of the outermost rocky or icy layer of a planet or moon. Whichever way the heat is discharged, knowing how much of it a planet pushes out is important because it could make or break habitability.

For instance, too much volcanic activity can turn a livable world into a molten nightmare. But too little activity can shut down the release of gases that make up an atmosphere, leaving a cold, barren surface. Just the right amount supports a livable, wet planet like Earth, or a possibly livable moon like Europa.

In the next decade, NASA's Europa Clipper will explore the surface and subsurface of Europa and provide insights about the environment beneath the surface. The more scientists can learn about Europa and other potentially habitable moons of our solar system, the better they'll be able to understand similar worlds around other stars -- which may be plentiful, according to today's findings.

"Forthcoming missions will give us a chance to see whether ocean moons in our solar system could support life," says Quick, who is a science team member on both the Clipper mission and the Dragonfly mission to Saturn's moon Titan. "If we find chemical signatures of life, we can try to look for similar signs at interstellar distances."

When Webb launches, scientists will try to detect chemical signatures in the atmospheres of some of the planets in the TRAPPIST-1 system, which is 39 light years away in the constellation Aquarius. In 2017, astronomers announced that this system has seven Earth-size planets. Some have suggested that some of these planets could be watery, and Quick's estimates support this idea. According to her team's calculations, TRAPPIST-1 e, f, g and h could be ocean worlds, which would put them among the 14 ocean worlds the scientists identified in this study.

The researchers predicted that these exoplanets have oceans by considering the surface temperatures of each one. This information is revealed by the amount of stellar radiation each planet reflects into space. Quick's team also took into account each planet's density and the estimated amount of internal heating it generates compared to Earth.

"If we see that a planet's density is lower than Earth's, that's an indication that there might be more water there and not as much rock and iron," Quick says. And if the planet's temperature allows for liquid water, you've got an ocean world.

"But if a planet's surface temperature is less than 32 degrees Fahrenheit (0 degrees Celsius), where water is frozen," Quick says, "then we have an icy ocean world, and the densities for those planets are even lower."

Credit: 
NASA/Goddard Space Flight Center

UC Davis study details use of extreme risk protection orders in Calif. over first four years

image: Map shows the number of Gun Violence Restraining Order respondents in California counties, 2016 to 2019.

Image: 
UC Davis Violence Prevention Program

(SACRAMENTO) --In the first four years since California established extreme risk protection order (ERPO) policies, use of the relatively new violence prevention tool has increased substantially, a UC Davis Violence Prevention Program (VPRP) study has found. The majority of orders were requested by law enforcement officers for recipients who are male and white.

In 2016, California enacted a gun violence restraining orders; these are known nationwide as extreme risk protection orders (ERPOs). The policies enable law enforcement as well as individual family or household members who observe a person's dangerous behavior to initiate a legal process that results in the temporary removal of that person's firearms and ammunition. That process also temporarily prevents the individual from legally purchasing firearms and ammunition.

ERPOs help fill a gap in violence prevention policy by allowing individuals to intervene when someone who is not prohibited from owning a firearm poses an immediate risk of violence to themselves or others. ERPOs are a tool for targeted violence prevention when other risk-reduction interventions - such as arrest on probable cause, domestic violence and other protective orders, and involuntary mental health hold - are not appropriate or have failed.

The UC Davis research, published today in JAMA Network Open, is one of the first to detail the early use of ERPOs in California, the first state to establish such policies. The population-based study described the characteristics of ERPO petitioners and the individuals subject to them, as well as the patterns of ERPO requests over time and geographically.

An invited commentary by practitioners seeing and enforcing ERPO policies describes the new VPRP study as "an important contribution to understanding state-level [ERPO] adoption."

"About 90% of the 1,076 individuals who were subject to an ERPO in 2016-2019 were male and about three-fifths were white," said Rocco Pallin, first author of the study and a VPRP researcher. "In nearly all cases, law enforcement officers filed the orders."

The authors report a substantial increase in use of ERPOs over the four-year study period, with the largest increase from 2018-2019. They also found differences in ERPO use by county and significant geographic clustering among neighboring counties.

"Media coverage and awareness of these policies raised by local public champions in areas with the highest ERPO use, like Southern California, may have played a role in the more rapid uptake in the last year of the study period," Pallin said.

Initial comparison of ERPO use in California in the early years of policy implementation with use in other states with such policies suggested slower uptake in California. The authors explained there might be factors affecting speed of uptake, including differences in the types of people who can initiate a petition, awareness of policies, law enforcement willingness to issue ERPOs, and other factors related to firearm culture to firearm-owner population. Additional research is needed to more carefully assess differences across states. To date, 19 states and the District of Columbia have ERPO or similar policies.

"ERPO laws, in California and elsewhere, have been established after mass shooting events, but evidence thus far points to their promise for preventing suicides, the overall leading cause of death from firearms in the U.S.," Pallin said. "More research will allow us to better understand how ERPOs are being used to prevent suicides as well as harm directed at others."

The researchers hope the study results will help inform policymakers and other stakeholders involved in implementing policies and outreach in California and in other states.

Credit: 
University of California - Davis Health

Strenuous daily exercise may shorten, not prolong, longevity

image: Kabuki artists showed lower survival compared with the other three types of traditional arts performers (based on data of Hayashi and Kezuka, Lifespan of Japanese traditional artists Harvard Dataverse, V1, 2020).

Image: 
Naoyuki Hayashi, Kazuhiro Kezuka

By analyzing longevity data for professional Japanese traditional artists, researchers at Tokyo Institute of Technology (Tokyo Tech) have found that Kabuki actors, known for their vigorous movements, surprisingly had shorter lifespans compared with other traditional arts performers who lead mostly sedentary lifestyles. The findings suggest that job-related strenuous exercise throughout life may not necessarily extend longevity.

Frequent exercise is often touted as key to leading a long and healthy life. But few studies have delved into comparisons in longevity between those who partake in vigorous physical activity and those who lead mostly sedentary lifestyles as a result of their occupation throughout their lives.

Now, Naoyuki Hayashi and Kazuhiro Kezuka of Tokyo Tech's Institute of Liberal Arts have conducted an unusual study that calls into question the idea that vigorous daily exercise positively correlates with longevity.

They compared the lifespans of four different groups of Japanese traditional arts performers by examining data from a total of 699 professional male artists, both living and dead, whose birth and death records are all publicly available. They hypothesized that Kabuki actors would lead longer lives owing to the high-level physical activity involved in their theatrical performances, compared with Sado, Rakugo and Nagauta practitioners, who are known to perform tea ceremonies, recount comic stories and play musical instruments while sitting, respectively.

Using a method called Kaplan-Meier analysis[1], they found that contrary to expectations, the lifespan of Kabuki actors was shorter than that of the other three types of traditional artists.

The researchers postulate that one reason for the shorter lifespans of Kabuki artists could be that excessive endurance training and physical activity overwhelms the beneficial aspects of regular physical exercise. Another reason might be that in the past, Kabuki actors have often worn oshiroi (white powder used for make-up) containing lead, which carries a significant health risk. The use of oshiroi was only banned in Japan in 1934.

The researchers point out their study is not without limitations. For example, the data examined male-dominated professions only, and therefore does not give a portrayal of population-wide longevity including females.

Further work would be needed to evaluate the optimal amount of exercise for protecting health. The possibly beneficial effects of "non-exercise" activities such as speaking, singing and playing musical instruments would also need further exploration.

Overall, the researchers say their study represents "a novel way of extracting information from publicly available data" and "contributes to the global trend in addressing reproducibility in science."

Credit: 
Tokyo Institute of Technology

Optogenetic odors reveal the logic of olfactory perception

Using optogenetic control, researchers have created an electrical signature that is perceived as an odor in the brain's smell-processing center, the olfactory bulb, even though the odor does not exist. Applied in the brains of mice, the approach proved useful in advancing our understanding of the neuronal logic of how mammalian brains perceive smells and distinguish one smell from the next. "Deciphering how the sense of smell works has recently received an interesting new twist for two reasons: a robust early symptom of COVID-19 is a loss of the sense of smell, and trained animals can potentially be trained to sniff out diseases," said lead author Edmund Chong. "Hence, a better understanding of the mechanisms of smell can potentially aid the design of powerful tools for disease detection and treatment during a pandemic." The science of sense seeks to understand the neural activity generated by sensory stimuli and how this activity creates and shapes the perception of the senses. Odors induce complex activity patterns in the olfactory bulb, a tiny structure located at the front of the brain. The combinations of individual neurons that respond to the stimuli - which can vary in both location and timing - are thought to underly how individual smells are perceived. However, untangling the complexities of such activity and understanding how it determines how a scent is perceived have been difficult. Edmund Chong and colleagues designed experiments based on the availability of mice genetically engineered by another lab so that their brain cells could be activated by shining light on them -- a technique called optogenetics. Next they trained the mice to recognize a signal generated by light activation of six glomeruli -- known to resemble a pattern evoked by an odor -- by giving them a water reward only when they perceived the correct "odor" and pushed a lever. If mice pushed the lever after activation of a different set of glomeruli (simulation of a different odor), they received no water. Using this model, the researchers changed the timing and mix of activated glomeruli. They found that changing which of the glomeruli within each odor-defining set were activated first led to as much as a 30 percent drop in the ability of a mouse to correctly sense an odor signal and obtain water. According to the results, the novel approach revealed key spatial and temporal neural features, which combined, offer a code of sorts for how the brain converts sensory information into perception of an odor.

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

Addressing the persistent gender gaps in some STEM pursuits

In a Policy Forum, Joseph Cimpian and colleagues identify blind spots in current educational policy designed to remedy gender inequity in STEM and argue that interventions may need to become more nuanced concerning student achievement. Not all STEM majors are equal in terms of gender disparity and despite educational efforts to equalize gender representation, significant gaps persist in some areas. While men and women are now nearly equally represented in biology, chemistry, mathematics and many other STEM college majors, men continue to outnumber women 4-to-1 in the fields of physics, engineering and computer science (PECS). Using the Department of Education's High School Longitudinal Study of 2009, which tracked nearly 6,000 students nationwide throughout their high school and college careers, Cimpian et al. evaluated the largely overlooked links between gender differences in achievement and the pursuit of PECS majors. According to the findings, low-achieving men join and persist in PECS majors at rates higher than far more qualified women. What's more, women who major in such fields are higher-achieving than their male peers. The patterns suggest that, while research and policy may be successful in encouraging high-achieving women into PECS pursuits, other factors may be discouraging average- and lower-achieving women from entering these fields, despite attracting lower-achieving men. Without addressing these factors, the persistent PECS gender gap is unlikely to fully close as it has in other STEM fields, say the authors.

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