thescientist--2020-08-12--Disturbed Microbes Contribute to Lung Damage from Oxygen Treatment

When a patient is suffering respiratory failure , such as can occur with COVID-19 , breathing oxygen-enriched air may save their life , but there ’ s a chance it may also damage their lungs .
The cause of the injury , at least in part , is an oxygen-induced shift in the balance of bacterial species in the lung , according to the results of a study in Science Translational Medicine today ( August 12 ) .
“ It ’ s an important paper in establishing that there is a role of the microbiome in hyperoxia-induced lung injury , @ @ @ @ @ @ @ University of Pittsburg who was not involved in the research .
The study “ opens the door to looking more closely at the impact [ of the microbiome ] and how we can modulate it ” for lung therapies , she continues .
“ It ’ s a really neat set of experiments .
They ’ ve taken a clinical conundrum , delved into human samples and then they ’ ve [ followed up with ] really elegant mouse models and mechanistic studies , ” adds lung disease researcher Philip Molyneaux of Imperial @ @ @ @ @ @ @ so vital for life , is well known to be toxic and potentially lethal to animals when given at high concentrations .
Concerns exist about oxygen ’ s widespread medical use too .
The gas is given to many patients with low blood oxygen levels but it has been linked to lung injury and pneumonia .
“ We ’ ve known about the damage caused by hyperoxia for a long time , ” says Leopoldo Segal , a lung microbiome researcher and critical care specialist at New York University who did not participate @ @ @ @ @ @ @ a major issue .
.
.
particularly pertinent during this COVID pandemic , because [ the patients ] are extremely refractory to oxygen and so they stay on high doses of oxygen for a very long time.
” It ’ s a balancing act between the known danger , Segal says , and the reality that “ the patients would be in trouble if they were at lower oxygen concentrations.
” How oxygen causes damage and why some patients fair worse than others was unclear .
Robert Dickson of the University of Michigan @ @ @ @ @ @ @ blame .
The lungs are populated with a community of microbes , Dickson explains , and “ oxygen is very important for bacteria ” in all sorts of ecosystems , not just the body .
Oxygen affects which ones will grow well and which won ’ t .
In the lungs , he continues , “ you have aerobes , you have anaerobes , so we had a strong intuition that oxygen would be a main driver of the lung ecology.
” To test their hypothesis the researchers examined the bacterial content of @ @ @ @ @ @ @ 1,500 patients between 2015 and 2018 who had been placed on a ventilator for at least 24 hours and exposed to low ( 21–43 percent ) medium ( 43–55 percent ) or high ( over 55 percent ) oxygen .
They found that , while the likelihood of detecting Staphylococcus aureus—the bacterium most often linked with ventilator-associated pneumonia—and Pseudomonas aeruginosa—another lung bacterium—was comparable in the low oxygen samples , S. aureus was detected twice as much as P. aeruginosa in the high-oxygen specimens .
In healthy mice , exposure to hyperoxia also resulted @ @ @ @ @ @ @ in the proportions of Staphylococcus species , the team showed .
These microbial population shifts preceded the occurrence of inflammation ( shown by increases in detectable cytokines ) and of lung injury ( shown by elevated levels of leaked protein in lung fluids ) .
While these results hinted that oxygen-induced microbiome changes cause injury , the team ’ s next experiment was the kicker , says Dickson .
It showed “ that if you take the microbiome out , you use germ-free mice that have absolutely no bacteria on or in their @ @ @ @ @ @ @ , they are protected .
They don ’ t get leaky lungs .
.
.
.
Under a microscope the lung tissue looks normal.
” This finding , Dickson says , “ argues that one way or another , the microbiome is actually playing a causal role in this lung injury.
” “ Up till now , we knew that we were causing damage , but there was nothing from a therapeutic standpoint that we have discovered that can prevent the damage , ” Segal says .
Now that there is a mechanism @ @ @ @ @ @ @ easily imagine that you can start intervening .
.
.
where you try to modify the existing microbiota in the setting of hyperoxia to decrease the harm.
” More experiments would be necessary to figure out if and how such microbial manipulations would work , says Segal , but antibiotics might not be sufficient .
The team showed that two regimens of antibiotics given to the hyperoxia-treated animals did nothing to protect them from lung damage , while a third drug worsened the lung damage .
While clinical practice is unlikely to change @ @ @ @ @ @ @ s results—after all , patients in respiratory failure still need oxygen and often need antibiotics—they do reinforce the message that “ oxygen is a drug and the administration of any drug needs to be done appropriately , ” says Molyneaux .
“ When you overdose someone with a drug , there are problems.
” S.L .
Ashley et al.
, “ Lung and gut microbiota are altered by hyperoxia and contribute to oxygen-induced lung injury in mice , ” Sci Transl Med , 12 : eaau9959 , 2020 .

“It’s an important paper in establishing that there is a role of the microbiome in hyperoxia-induced lung injury,” says pulmonologist Alison Morris of the University of Pittsburg who was not involved in the research. The study “opens the door to looking more closely at the impact [of the microbiome] and how we can modulate it” for lung therapies, she continues.
When a patient is suffering respiratory failure, such as can occur with COVID-19, breathing oxygen-enriched air may save their life, but there’s a chance it may also damage their lungs. The cause of the injury, at least in part, is an oxygen-induced shift in the balance of bacterial species in the lung, according to the results of a study in Science Translational Medicine today (August 12).
Oxygen, an element so vital for life, is well known to be toxic and potentially lethal to animals when given at high concentrations. Concerns exist about oxygen’s widespread medical use too. The gas is given to many patients with low blood oxygen levels but it has been linked to lung injury and pneumonia.
“We’ve known about the damage caused by hyperoxia for a long time,” says Leopoldo Segal, a lung microbiome researcher and critical care specialist at New York University who did not participate in the research. “It is a major issue . . . particularly pertinent during this COVID pandemic, because [the patients] are extremely refractory to oxygen and so they stay on high doses of oxygen for a very long time.” It’s a balancing act between the known danger, Segal says, and the reality that “the patients would be in trouble if they were at lower oxygen concentrations.”
How oxygen causes damage and why some patients fair worse than others was unclear. Robert Dickson of the University of Michigan and colleagues suspected bacteria might be to blame. The lungs are populated with a community of microbes, Dickson explains, and “oxygen is very important for bacteria” in all sorts of ecosystems, not just the body. Oxygen affects which ones will grow well and which won’t. In the lungs, he continues, “you have aerobes, you have anaerobes, so we had a strong intuition that oxygen would be a main driver of the lung ecology.”
You can easily imagine that you can start intervening . . . where you try to modify the existing microbiota in the setting of hyperoxia to decrease the harm. —Leopoldo Segal, New York University
To test their hypothesis the researchers examined the bacterial content of lung fluid specimens procured from more than 1,500 patients between 2015 and 2018 who had been placed on a ventilator for at least 24 hours and exposed to low (21–43 percent) medium (43–55 percent) or high (over 55 percent) oxygen. They found that, while the likelihood of detecting Staphylococcus aureus—the bacterium most often linked with ventilator-associated pneumonia—and Pseudomonas aeruginosa—another lung bacterium—was comparable in the low oxygen samples, S. aureus was detected twice as much as P. aeruginosa in the high-oxygen specimens.
In healthy mice, exposure to hyperoxia also resulted in altered microbiome compositions, including increases in the proportions of Staphylococcus species, the team showed. These microbial population shifts preceded the occurrence of inflammation (shown by increases in detectable cytokines) and of lung injury (shown by elevated levels of leaked protein in lung fluids).
While these results hinted that oxygen-induced microbiome changes cause injury, the team’s next experiment was the kicker, says Dickson. It showed “that if you take the microbiome out, you use germ-free mice that have absolutely no bacteria on or in their body, and you give them hyperoxia, they are protected. They don’t get leaky lungs. . . . Under a microscope the lung tissue looks normal.”
This finding, Dickson says, “argues that one way or another, the microbiome is actually playing a causal role in this lung injury.”
“Up till now, we knew that we were causing damage, but there was nothing from a therapeutic standpoint that we have discovered that can prevent the damage,” Segal says. Now that there is a mechanism, he says, “you can easily imagine that you can start intervening . . . where you try to modify the existing microbiota in the setting of hyperoxia to decrease the harm.”
More experiments would be necessary to figure out if and how such microbial manipulations would work, says Segal, but antibiotics might not be sufficient. The team showed that two regimens of antibiotics given to the hyperoxia-treated animals did nothing to protect them from lung damage, while a third drug worsened the lung damage.
While clinical practice is unlikely to change on the strength of the paper’s results—after all, patients in respiratory failure still need oxygen and often need antibiotics—they do reinforce the message that “oxygen is a drug and the administration of any drug needs to be done appropriately,” says Molyneaux. “When you overdose someone with a drug, there are problems.”
S.L. Ashley et al., “Lung and gut microbiota are altered by hyperoxia and contribute to oxygen-induced lung injury in mice,” Sci Transl Med, 12:eaau9959, 2020.


thescientist--2020-08-12--August 2020 Interactive Crossword Puzzle

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thescientist--2020-08-12--Trials Seek to Answer if Vitamin D Could Help in COVID-19

A few years back , respiratory physician Adrian Martineau of Queen Mary University of London and colleagues analyzed data from about 11,000 participants in 25 trials that tested the effect of vitamin D supplementation on the risk of contracting an acute respiratory tract infection such as influenza .
They determined that taking a daily or weekly dose of vitamin D was protective against infections and safe overall .
People with the lowest starting vitamin D levels benefitted the most from supplementation .
When David Meltzer , an internist and economist at the University of Chicago , saw that analysis earlier @ @ @ @ @ @ @ into a possible connection between vitamin D and COVID-19 .
There was good reason to do so .
Groups who are often low in vitamin D—such as African Americans , who tend to have darker skin in which higher melanin levels limit UV rays from fueling vitamin D production , and the elderly—were being hit especially hard by the disease .
Meltzer and his colleagues went back through the medical records of people who had been tested for COVID-19 in Chicago between March 3 and April 10 and measured the relationship between vitamin @ @ @ @ @ @ @ positive tests .
“ The people who were vitamin D deficient were dramatically more likely to have COVID than the people who weren ’ t vitamin D deficient , ” says Meltzer , who , along with his coauthors , published the results as a preprint on medRxiv in May .
Another study from Israel , published July 23 in The FEBS Journal , likewise found a link between low levels of vitamin D and increased COVID-19 susceptibility .
Such correlative evidence has fueled studies on whether vitamin D supplementation can prevent or @ @ @ @ @ @ @ of open questions .
For one , too much vitamin D can lead to an excess of calcium in the blood and , in severe cases , organ damage , so determining the correct amount to give will be essential .
And the correlational evidence doesn ’ t all agree .
For instance , a study of people in the United Kingdom published in May in Diabetes & Metabolic Syndrome : Clinical Research & Reviews did not find evidence for a link between vitamin D levels and getting COVID-19 or having a poorer @ @ @ @ @ @ @ evidence , it ’ s not clear whether the supplement is right for everyone .
Meltzer adds that it ’ s also not clear whether vitamin D deficiency is causing or reflecting individuals ’ increased susceptibility .
There are lots of reasons—including age , chronic illness , and spending time indoors—why low vitamin D could be correlated with the likelihood of testing positive , Meltzer explains .
In the study , the researchers controlled for these potentially confounding factors , “ but we can ’ t control for everything , ” he says @ @ @ @ @ @ @ or not vitamin D can prevent COVID-19 is to perform randomized controlled trials , he adds—something he and his colleagues are working on in multiple populations , including first responders .
Carol Wagner , a neonatologist at the Medical University of South Carolina , has studied vitamin D in clinical trials since 2000 , often in pregnant and lactating women .
Initially , researchers thought that vitamin D ’ s role in the body was limited to its functions in bone health and calcium metabolism , she says , and the ways in @ @ @ @ @ @ @ ignored .
“ When you start looking at differences in immune function of those who are vitamin D replete versus those who are not , you see really clear , elegant work from many labs around the globe identifying vitamin D ’ s role in not only innate but adaptive immunity , ” she says .
And more people these days are vitamin D deficient because we now spend much more time inside and use sunscreen—both of which limit exposure to the sun ’ s UV rays , a prime source of vitamin @ @ @ @ @ @ @ has been confirmed in clinical studies demonstrating that people with lower levels of vitamin D are more prone to infections , both bacterial and viral , and by lab-based findings demonstrating that vitamin D upregulates the expression of immune-related genes .
Based on this evidence , Wagner and colleagues began recruiting participants in July for a randomized clinical trial to investigate whether vitamin D supplements can help prevent COVID-19 or lessen the disease ’ s severity .
Theirs is just one of about 30 entries on clinicaltrials.gov that either explore the link between @ @ @ @ @ @ @ or test the effectiveness of vitamin D supplements in preventing or treating the disease .
Similar studies that aren ’ t referenced in clinicaltrials.gov are in the works , including a large , population-based trial Queen Mary University ’ s Martineau and colleagues are setting up now .
“ From the lab , there ’ s a convincing story that vitamin D should be beneficial .
It ’ s doing the right sort of stuff , in terms of upregulating a whole host of innate antiviral immune mechanisms and also simultaneously dampening down @ @ @ @ @ @ @ are particularly harmful , ” Martineau explains .
Clinical trials are still necessary , he says , because “ there ’ s a lot of observational data out there linking lower vitamin D levels to either heightened susceptibility or poorer outcomes , but these are limited in quality in that they can ’ t really pull apart confounding or reverse causality , which could also explain these associations.
” Getting the dose right Part of the challenge in sussing out the role of vitamin D in the prevention and treatment of viral infections @ @ @ @ @ @ @ of generalizability of previous clinical trials , says Jill Weatherhead , an infectious disease physician at Baylor College of Medicine .
“ There are differences in methodology , differences in vitamin D supplement regimens , [ and ] differences in participant characterization.
” The current clinical trials to evaluate the link between vitamin D and COVID-19 also differ in some of these aspects .
In the MUSC trial , people 50 years and older will be tested for COVID-19 .
If they ’ re negative , they ’ ll receive either 6,000 international @ @ @ @ @ @ @ vitamin D or a placebo daily .
If they test positive , they ’ ll get a bolus of 20,000 IU or a placebo bolus once a day for three days and then 6,000 IU or placebos daily after .
Each participant in both the test and control groups will also get a daily multivitamin containing 800 IU of vitamin D. The 6,000 IU daily dose and 20,000 IU bolus are both doses that have been shown to be safe in previous work .
In trials being planned by Martineau and colleagues in @ @ @ @ @ @ @ be lower , based on an update to their 2017 meta-analysis that they posted on medRxiv in July .
They used primary data from more than 29,000 patients in 39 randomized trials to determine that the daily dose of vitamin D that provides the best protection against respiratory infections is between 400 and 1,000 IU .
“ Until we ’ d done this exercise , I would have been saying that something like two to four thousand [ IU ] a day is probably optimal—just from the grounds that it takes vitamin D @ @ @ @ @ @ @ , but actually , based on the data that we got there , it seems like a moderate dose is potentially more effective than these much higher doses that some people have been promoting , ” Martineau says .
It ’ s important to “ highlight , though , that this is for acute respiratory infections in general .
None of these studies would have been done in COVID , so you can ’ t generalize too enthusiastically.
” Part of the issue with dosing , according to Meltzer , is that it @ @ @ @ @ @ @ of vitamin D are .
The daily recommended dietary allowance from the Institute of Medicine of the National Academies is 600–800 IU of vitamin D for adults , he says , but “ if you look at people who are out in the sun all the time , like lifeguards , they have higher vitamin D levels .
.
.
probably twice or more than what they are in the average American .
Yet , most of those people don ’ t have any problem at all with high calcium levels , ” @ @ @ @ @ @ @ of taking too much of the vitamin .
“ I ’ m not advocating that people take ten thousand units a day in an uncontrolled environment , but do I think it ’ s in the realm of what should be studied ?
Absolutely , ” he continues , adding that there ’ s also the possibility that a dose that ’ s too low could end up in a subtherapeutic range .
Until the results of clinical trials are available , “ people need to be cautious about what vitamins and supplements @ @ @ @ @ @ @ cause harm , ” Weatherhead cautions , pointing to the possible side effects , as well as potential interactions of vitamin D with other drugs people might be taking .
“ Use of supplements with the recommended daily intake is not an unreasonable approach , ” she adds .
“ It ’ s a balance.
” “ We know that vitamin D is good for bones and muscles , ” says Martineau .
“ Therefore , it makes sense to take a bit , and it might just help against COVID , too @ @

When David Meltzer, an internist and economist at the University of Chicago, saw that analysis earlier this year, he decided to look into a possible connection between vitamin D and COVID-19. There was good reason to do so. Groups who are often low in vitamin D—such as African Americans, who tend to have darker skin in which higher melanin levels limit UV rays from fueling vitamin D...
A few years back, respiratory physician Adrian Martineau of Queen Mary University of London and colleagues analyzed data from about 11,000 participants in 25 trials that tested the effect of vitamin D supplementation on the risk of contracting an acute respiratory tract infection such as influenza. They determined that taking a daily or weekly dose of vitamin D was protective against infections and safe overall. People with the lowest starting vitamin D levels benefitted the most from supplementation.
Another study from Israel, published July 23 in The FEBS Journal, likewise found a link between low levels of vitamin D and increased COVID-19 susceptibility.
Such correlative evidence has fueled studies on whether vitamin D supplementation can prevent or treat COVID-19, but there are plenty of open questions. For one, too much vitamin D can lead to an excess of calcium in the blood and, in severe cases, organ damage, so determining the correct amount to give will be essential. And the correlational evidence doesn’t all agree. For instance, a study of people in the United Kingdom published in May in Diabetes & Metabolic Syndrome: Clinical Research & Reviews did not find evidence for a link between vitamin D levels and getting COVID-19 or having a poorer prognosis afterwards. Based on the conflicting evidence, it’s not clear whether the supplement is right for everyone.
Meltzer adds that it’s also not clear whether vitamin D deficiency is causing or reflecting individuals’ increased susceptibility. There are lots of reasons—including age, chronic illness, and spending time indoors—why low vitamin D could be correlated with the likelihood of testing positive, Meltzer explains. In the study, the researchers controlled for these potentially confounding factors, “but we can’t control for everything,” he says.
The best way to determine whether or not vitamin D can prevent COVID-19 is to perform randomized controlled trials, he adds—something he and his colleagues are working on in multiple populations, including first responders.
Immunity and vitamin D
Carol Wagner, a neonatologist at the Medical University of South Carolina, has studied vitamin D in clinical trials since 2000, often in pregnant and lactating women. Initially, researchers thought that vitamin D’s role in the body was limited to its functions in bone health and calcium metabolism, she says, and the ways in which it affects immune function were mostly ignored.
“When you start looking at differences in immune function of those who are vitamin D replete versus those who are not, you see really clear, elegant work from many labs around the globe identifying vitamin D’s role in not only innate but adaptive immunity,” she says. And more people these days are vitamin D deficient because we now spend much more time inside and use sunscreen—both of which limit exposure to the sun’s UV rays, a prime source of vitamin D.
Based on the data that we got there, it seems like a moderate dose is potentially more effective than these much higher doses that some people have been promoting. —Adrian Martineau, Queen Mary University of London
An immune role for vitamin D has been confirmed in clinical studies demonstrating that people with lower levels of vitamin D are more prone to infections, both bacterial and viral, and by lab-based findings demonstrating that vitamin D upregulates the expression of immune-related genes. Based on this evidence, Wagner and colleagues began recruiting participants in July for a randomized clinical trial to investigate whether vitamin D supplements can help prevent COVID-19 or lessen the disease’s severity.
Theirs is just one of about 30 entries on clinicaltrials.gov that either explore the link between low levels of vitamin D and COVID-19 or test the effectiveness of vitamin D supplements in preventing or treating the disease. Similar studies that aren’t referenced in clinicaltrials.gov are in the works, including a large, population-based trial Queen Mary University’s Martineau and colleagues are setting up now.
“From the lab, there’s a convincing story that vitamin D should be beneficial. It’s doing the right sort of stuff, in terms of upregulating a whole host of innate antiviral immune mechanisms and also simultaneously dampening down inflammatory responses that we know in COVID-19 are particularly harmful,” Martineau explains. Clinical trials are still necessary, he says, because “there’s a lot of observational data out there linking lower vitamin D levels to either heightened susceptibility or poorer outcomes, but these are limited in quality in that they can’t really pull apart confounding or reverse causality, which could also explain these associations.”
Getting the dose right
Part of the challenge in sussing out the role of vitamin D in the prevention and treatment of viral infections comes from the heterogeneity and the lack of generalizability of previous clinical trials, says Jill Weatherhead, an infectious disease physician at Baylor College of Medicine. “There are differences in methodology, differences in vitamin D supplement regimens, [and] differences in participant characterization.”
The current clinical trials to evaluate the link between vitamin D and COVID-19 also differ in some of these aspects. In the MUSC trial, people 50 years and older will be tested for COVID-19. If they’re negative, they’ll receive either 6,000 international units (IU)—about 150 micrograms—of vitamin D or a placebo daily. If they test positive, they’ll get a bolus of 20,000 IU or a placebo bolus once a day for three days and then 6,000 IU or placebos daily after. Each participant in both the test and control groups will also get a daily multivitamin containing 800 IU of vitamin D. The 6,000 IU daily dose and 20,000 IU bolus are both doses that have been shown to be safe in previous work.
People need to be cautious about what vitamins and supplements they’re taking because some do cause harm. —Jill Weatherhead, Baylor College of Medicine
In trials being planned by Martineau and colleagues in the UK, the dose will likely be lower, based on an update to their 2017 meta-analysis that they posted on medRxiv in July. They used primary data from more than 29,000 patients in 39 randomized trials to determine that the daily dose of vitamin D that provides the best protection against respiratory infections is between 400 and 1,000 IU.
“Until we’d done this exercise, I would have been saying that something like two to four thousand [IU] a day is probably optimal—just from the grounds that it takes vitamin D status more reliably to the therapeutic range, but actually, based on the data that we got there, it seems like a moderate dose is potentially more effective than these much higher doses that some people have been promoting,” Martineau says. It’s important to “highlight, though, that this is for acute respiratory infections in general. None of these studies would have been done in COVID, so you can’t generalize too enthusiastically.”
Part of the issue with dosing, according to Meltzer, is that it’s not clear what optimal levels of vitamin D are. The daily recommended dietary allowance from the Institute of Medicine of the National Academies is 600–800 IU of vitamin D for adults, he says, but “if you look at people who are out in the sun all the time, like lifeguards, they have higher vitamin D levels . . . probably twice or more than what they are in the average American. Yet, most of those people don’t have any problem at all with high calcium levels,” which is one of the possible dangers of taking too much of the vitamin.
“I’m not advocating that people take ten thousand units a day in an uncontrolled environment, but do I think it’s in the realm of what should be studied? Absolutely,” he continues, adding that there’s also the possibility that a dose that’s too low could end up in a subtherapeutic range.
Until the results of clinical trials are available, “people need to be cautious about what vitamins and supplements they’re taking because some do cause harm,” Weatherhead cautions, pointing to the possible side effects, as well as potential interactions of vitamin D with other drugs people might be taking. “Use of supplements with the recommended daily intake is not an unreasonable approach,” she adds. “It’s a balance.”
“We know that vitamin D is good for bones and muscles,” says Martineau. “Therefore, it makes sense to take a bit, and it might just help against COVID, too.”


thescientist--2020-08-12--Simple Tool Evaluates Mask Performance at Blocking Droplets

Masks have emerged as one of the most important public health initiatives of the COVID-19 pandemic , but they come in so many forms , it can be difficult to know which ones work best at blocking respiratory droplets and tiny airborne spray .
A study published August 7 in Science Advances as a proof of concept details a new method for easily visualizing the droplets emitted while speaking and the rough efficiency of different types of masks in minimizing their spread .
The authors used a cheap but powerful laser to create a screen of light that scatters when @ @ @ @ @ @ @ or so masks they tested , some did a much better job at dampening the number of particles detected by the laser .
“ We know that all masks are not created equal , ” Erica Shenoy , the associate chief of the infection control unit at Massachusetts General Hospital who was not involved in the study , tells The Scientist in an email .
“ This study corroborates differences in relative performance of many of the types of masks that we are all seeing every day when out and about in public.
@ @ @ @ @ @ @ when an out-of-work ballet costume designer sent Eric Westman , a specialist in obesity medicine at Duke University Health System , a message on social media .
She had heard that Westman was working to source and manufacture masks for vulnerable citizens , and she wanted to offer her team of unemployed costume makers .
“ These people who are used to using these fabrics for ballroom costumes .
.
.
were now using this beautiful material ” to make masks , Westman says .
See “ How Face Masks Prevent the Spread @ @ @ @ @ @ @ way to test the effectiveness of the different materials , so he picked up the phone and called the physics department at Duke University .
Martin Fischer , an expert in biomedical imaging , took up the challenge , bringing in his college-aged daughter so the two could work closely without fear of passing the virus to others .
Together , they built a simple tool out of a cardboard box , a laser , a lens , and a smartphone camera capable of capturing visible evidence of airborne particles .
Fischer used @ @ @ @ @ @ @ beam of the laser into a thin “ light sheet , ” passing it through slits in the sides of a blackened box .
When a person speaks into the box , the particles cross through the light sheet , scattering the light in different directions .
A camera on the other end records that scatter , which appears on the video as winking green lights , and a simple computer algorithm tallies the number of droplets and the rate at which they pass through the sheet .
The whole setup costs just @ @ @ @ @ @ @ it ’ s really important what they were able to do in terms of using a laser light scattering method that can be implemented cheaply and easily , so that people can really see the effect , ” Christina Bax , a medical student at the University of Pennsylvania who was not involved in the research , tells The Scientist .
Earlier this year , Bax had independently developed a similar technique , and found that when speaking , “ everybody has saliva droplets flying everywhere.
” Fischer ’ s team tested the @ @ @ @ @ @ @ the spread of those droplets , including the medical grade N95s ( with and without valves ) used by frontline healthcare workers , disposable blue surgical masks , hand-sewn cotton masks , neck fleeces , and bandanas , among others .
A single person spoke the phrase “ stay healthy , people ” five times in a row into the box , a process that was repeated 10 times for each mask and for the no-mask control .
The results , Fisher says , were “ an eye opener for how many of @ @ @ @ @ @ @ when people are just talking .
When speaking without masks , Westman and Fischer found that people exhale hundreds of drops per second , many of which are too small to be detected by the naked eye but still flashed green inside the box .
Among the many masks they tested , the N95 with no valve performed best , with only 0.1 percent of the particles making it through the light sheet ; the version with the valve may do a good job of protecting the wearer , but it still allows @ @ @ @ @ @ @ out .
Hand-sewn cotton masks composed of at least two layers also performed well , as did single-use surgical masks , vastly decreasing the number of particles spreading into the air while talking .
But cotton bandanas and Buff-type neck gaiters made of spandex performed poorly , and in fact sometimes caused more drops to pass across the beam than had been detected in the control .
The authors attribute this finding to a sort of cheese grater effect : larger particles passing through the porous material were broken up into smaller aerosols @ @ @ @ @ @ @ is better than nothing , ” Westman says .
“ But the idea that it ’ s a mesh can change the dynamic.
” This study is only a proof of concept meant to show the utility of the laser setup and not to draw broad conclusions about the efficacy of different masks .
The researchers sampled only what was at hand and used only one speaker to test all 14 types .
It is likely , the authors say , that variations between individuals based on tone , volume , enunciation , @ @ @ @ @ @ @ differences in fabric quality and the fit of a mask , might change their findings .
If backed up by further study , the results suggest that scarce N95 masks are best left for frontline workers , as average citizens can make do with masks made at home .
In addition to the relatively small sample size , Shenoy adds , it is possible that not all droplets were captured in the count due to the experimental set up and limitations in the detection sensitivity of the cell phone camera , especially for @ @ @ @ @ @ @ Exhalations Help Spread Pathogens Such as SARS-CoV-2 ” The authors , who are currently attempting to patent their new product , envision it being used in public community centers or museums as an educational tool to show people why masks are so important and how best to wear them .
In addition , it may be useful for companies manufacturing masks to easily test the efficacy of their product , or in resource-poor countries as a cheaper alternative to costly laser particle sorters .
According to Bax , “ it comes back to @ @ @ @ @ @ @ what is happening , visualize the droplets , and understand that everybody spits when they speak .
”

A study published August 7 in Science Advances as a proof of concept details a new method for easily visualizing the droplets emitted while speaking and the rough efficiency of different types of masks in minimizing their spread. The authors used a cheap but powerful laser to create a screen of light that scatters when particles pass through. Of the dozen or so masks they tested, some did a much better job at dampening the number of particles detected by the laser.
Masks have emerged as one of the most important public health initiatives of the COVID-19 pandemic, but they come in so many forms, it can be difficult to know which ones work best at blocking respiratory droplets and tiny airborne spray.
The impetus for the project came when an out-of-work ballet costume designer sent Eric Westman, a specialist in obesity medicine at Duke University Health System, a message on social media. She had heard that Westman was working to source and manufacture masks for vulnerable citizens, and she wanted to offer her team of unemployed costume makers. “These people who are used to using these fabrics for ballroom costumes . . . were now using this beautiful material” to make masks, Westman says.
Westman needed a simple way to test the effectiveness of the different materials, so he picked up the phone and called the physics department at Duke University. Martin Fischer, an expert in biomedical imaging, took up the challenge, bringing in his college-aged daughter so the two could work closely without fear of passing the virus to others.
Together, they built a simple tool out of a cardboard box, a laser, a lens, and a smartphone camera capable of capturing visible evidence of airborne particles. Fischer used a cylindrical lens to stretch the pencil-like beam of the laser into a thin “light sheet,” passing it through slits in the sides of a blackened box. When a person speaks into the box, the particles cross through the light sheet, scattering the light in different directions. A camera on the other end records that scatter, which appears on the video as winking green lights, and a simple computer algorithm tallies the number of droplets and the rate at which they pass through the sheet. The whole setup costs just under $200.
Duke health
“I think it’s really important what they were able to do in terms of using a laser light scattering method that can be implemented cheaply and easily, so that people can really see the effect,” Christina Bax, a medical student at the University of Pennsylvania who was not involved in the research, tells The Scientist. Earlier this year, Bax had worked with colleagues at NIH who developed a similar technique, and found that when speaking, “everybody has saliva droplets flying everywhere.”
Fischer’s team tested the ability of 14 different masks to dampen the spread of those droplets, including the medical grade N95s (with and without valves) used by frontline healthcare workers, disposable blue surgical masks, hand-sewn cotton masks, neck fleeces, and bandanas, among others. A single person spoke the phrase “stay healthy, people” five times in a row into the box, a process that was repeated 10 times for each mask and for the no-mask control.
The results, Fisher says, were “an eye opener for how many of those particles are floating around” even when people are just talking. When speaking without masks, Westman and Fischer found that people exhale hundreds of drops per second, many of which are too small to be detected by the naked eye but still flashed green inside the box.
Among the many masks they tested, the N95 with no valve performed best, with only 0.1 percent of the particles making it through the light sheet; the version with the valve may do a good job of protecting the wearer, but it still allows particles to escape when a person breathes out. Hand-sewn cotton masks composed of at least two layers also performed well, as did single-use surgical masks, vastly decreasing the number of particles spreading into the air while talking.
But cotton bandanas and Buff-type neck gaiters made of spandex performed poorly, and in fact sometimes caused more drops to pass across the beam than had been detected in the control. The authors attribute this finding to a sort of cheese grater effect: larger particles passing through the porous material were broken up into smaller aerosols. “I came in thinking anything is better than nothing,” Westman says. “But the idea that it’s a mesh can change the dynamic.”
This study is only a proof of concept meant to show the utility of the laser setup and not to draw broad conclusions about the efficacy of different masks. The researchers sampled only what was at hand and used only one speaker to test all 14 types. It is likely, the authors say, that variations between individuals based on tone, volume, enunciation, and even language, as well as differences in fabric quality and the fit of a mask, might change their findings. If backed up by further study, the results suggest that scarce N95 masks are best left for frontline workers, as average citizens can make do with masks made at home.
In addition to the relatively small sample size, Shenoy adds, it is possible that not all droplets were captured in the count due to the experimental set up and limitations in the detection sensitivity of the cell phone camera, especially for smaller particles.
The authors, who are currently attempting to patent their new product, envision it being used in public community centers or museums as an educational tool to show people why masks are so important and how best to wear them. In addition, it may be useful for companies manufacturing masks to easily test the efficacy of their product, or in resource-poor countries as a cheaper alternative to costly laser particle sorters. According to Bax, “it comes back to this idea of being able to visualize what is happening, visualize the droplets, and understand that everybody spits when they speak.”


thescientist--2020-08-13--Coronavirus Found on Food Packaging, but Likely of Little Concern

There is growing evidence that food packaging is transporting SARS-CoV-2 across international borders .
Several countries are linked to either exported or imported frozen food that tested positive for traces of the virus , but experts say they believe the risk of developing COVID-19 from handling these products remains extremely low .
“ The number of virus particles coming out a person ’ s mouth or nose is far greater than a few virus particles remaining on frozen foods , somebody touching it and then spreading it , ” T. Jacob John , a retired virologist at Christian Medical College @ @ @ @ @ @ @ the risks , I think these are very low risks.
” China has reported the most cases of packaging contamination , according to NBC News , due in part to a massive screening effort targeting imported goods across the country .
Last month , Chinese health officials found traces of the coronavirus on frozen goods imported into the cities of Dalian , Xiamen , and Pingxiang .
In the last four days , similar findings have been reported in Wuhu and Shenzhen , linked to frozen shrimp and chicken wings imported from Ecuador @ @ @ @ @ @ @ frozen seafood of unnamed origins arriving in the port city of Yantai .
After New Zealand reported its first new cases of COVID-19 in more than three months , contact tracing revealed that one of the infected people worked in an import receiving facility , The Guardian reports .
As a result , public officials are considering the possibility that the virus arrived in the country on freight .
The facility is currently being tested to rule it out .
“ We can see the seriousness of the situation we are in , @ @ @ @ @ @ @ a news conference .
“ It ’ s being dealt with in an urgent but calm and methodical way.
” Previous research has shown that the virus can remain on packaging for hours or even days , depending on the type of material and the ambient conditions .
For paper and plastic , the materials related to the most recent reports , that time varies between four to five days , Reuters reports , although other studies have given different ranges .
Among the cases in China and New Zealand , it ’ @ @ @ @ @ @ @ virus was introduced onto the contaminated surfaces .
It could have happened at any point along the transport chain .
See “ SARS-CoV-2 Can Live on Plastic and Steel for 2–3 Days ” Both the World Health Organization ( WHO ) and the US Centers for Disease Control and Prevention ( CDC ) dismiss the idea that disease transmission on packaging is a serious concern .
The WHO says it is “ highly unlikely that people can contract Covid-19 from food or food packaging , ” due to the fact that coronaviruses require @ @ @ @ @ @ @ a body , they gradually become weaker and lose the ability to actively infect .
In a June memo , the CDC similarly claimed that the risk of infection from food products or bags is “ thought to be very low.
” Remnants of dead virus have been known to cause false positive results in recovered patients , CNN reports .
Researchers have taken to scientific journals to downplay transmission by fomites , a term for the surfaces themselves .
In a recent commentary in The Lancet , Emanuel Goldman , a microbiologist @ @ @ @ @ @ @ said , “ the chance of transmission through inanimate surfaces is very small , and only in instances where an infected person coughs or sneezes on the surface , and someone else touches that surface soon after.
” Speaking to The Atlantic in July , Goldman stated his position more emphatically : “ Surface transmission of COVID-19 is not justified at all by the science .
”

China has reported the most cases of packaging contamination, according to NBC News , due in part to a massive screening effort targeting imported goods across the country. Last month, Chinese health officials found traces of the coronavirus on frozen goods...
“The number of virus particles coming out a person’s mouth or nose is far greater than a few virus particles remaining on frozen foods, somebody touching it and then spreading it,” T. Jacob John, a retired virologist at Christian Medical College, tells Reuters . “Among all the risks, I think these are very low risks.”
There is growing evidence that food packaging is transporting SARS-CoV-2 across international borders. Several countries are linked to either exported or imported frozen food that tested positive for traces of the virus, but experts say they believe the risk of developing COVID-19 from handling these products remains extremely low.
After New Zealand reported its first new cases of COVID-19 in more than three months, contact tracing revealed that one of the infected people worked in an import receiving facility, The Guardian reports. As a result, public officials are considering the possibility that the virus arrived in the country on freight. The facility is currently being tested to rule it out. “We can see the seriousness of the situation we are in,” Prime Minister Jacinda Ardern said in a news conference. “It’s being dealt with in an urgent but calm and methodical way.”
Previous research has shown that the virus can remain on packaging for hours or even days, depending on the type of material and the ambient conditions. For paper and plastic, the materials related to the most recent reports, that time varies between four to five days, Reuters reports, although other studies have given different ranges. Among the cases in China and New Zealand, it’s difficult to know just when the virus was introduced onto the contaminated surfaces. It could have happened at any point along the transport chain.
Both the World Health Organization (WHO) and the US Centers for Disease Control and Prevention (CDC) dismiss the idea that disease transmission on packaging is a serious concern.
The WHO says it is “highly unlikely that people can contract Covid-19 from food or food packaging,” due to the fact that coronaviruses require a living host to multiply. Outside a body, they gradually become weaker and lose the ability to actively infect. In a June memo, the CDC similarly claimed that the risk of infection from food products or bags is “thought to be very low.” Remnants of dead virus have been known to cause false positive results in recovered patients, CNN reports.
Researchers have taken to scientific journals to downplay transmission by fomites, a term for the surfaces themselves. In a recent commentary in The Lancet, Emanuel Goldman, a microbiologist at Rutgers New Jersey Medical School, said, “the chance of transmission through inanimate surfaces is very small, and only in instances where an infected person coughs or sneezes on the surface, and someone else touches that surface soon after.”
Speaking to The Atlantic in July, Goldman stated his position more emphatically: “Surface transmission of COVID-19 is not justified at all by the science.”


thescientist--2020-08-13--Infectious Disease Researcher Steve Meshnick Dies

pidemiologist Steve Meshnick , whose work on malaria and other tropical diseases left a lasting effect on public health research in multiple African and Asian countries , died from cancer last week ( August 5 ) .
He was 68 .
A leading researcher on the mechanisms of action of antimalarial drugs such as artemisinin , Meshnick developed long-lasting scientific connections to the Democratic Republic of Congo ( DRC ) , Malawi , Thailand , and Cambodia , among other countries .
He helped to conduct training and build research capacity in these countries alongside his work at the University @ @ @ @ @ @ @ Chapel Hill , where he was based for the last two decades .
“ Steve was remarkable in every possible way , ” Myron Cohen , director of the Institute for Global Health and Infectious Diseases at UNC , says in a statement .
“ He was always excited about science and new ideas .
He inspired a generation of young investigators and built a world-class research team .
He loved working with people from around the globe .
He was a wonderful friend and colleague and he will be so sorely missed.
@ @ @ @ @ @ @ 1952 , Meshnick completed an undergraduate degree in biochemistry at Columbia University in 1972 , before earning graduate degrees in medical biochemistry at Rockefeller University and medicine at Cornell University in 1978 and 1979 , respectively .
After a number of appointments in the US and abroad—including one as a visiting scientist at the International Laboratory for Research in Animal Diseases in Nairobi in 1978—Meshnick took up a faculty position in 1992 at the University of Michigan , where he would remain for nearly 10 years before moving to UNC .
Over the @ @ @ @ @ @ @ published more than 350 scientific articles , at least 100 of which focused on drug resistance in tropical pathogens .
In particular , he was a proponent of using molecular and genetic tools in epidemiology , becoming an early adopter of techniques such as real-time PCR for detecting infections with Plasmodium falciparum , the parasite that causes malaria .
Some of his best known work was on the mechanisms of action of the antimalarial drug artemisinin .
In a number of papers published in the 1990s , he and colleagues in the US @ @ @ @ @ @ @ with proteins and other compounds in Plasmodium and reported that it binds to several different parasite proteins—a conclusion complemented by recent findings from other researchers that the drug blocks multiple cellular pathways in the parasite .
See “ Are We Headed for a New Era of Malaria Drug Resistance ?
” Throughout his career , Meshnick formed sustained relationships with scientists in other countries .
In the early 2000s , he established a partnership with researchers in the DRC , and recently committed funds he received from a UNC award for mentoring to @ @ @ @ @ @ @ collaborator .
An epidemiological project he helped establish in Kinshasa that has now recruited more than 1,600 participants is continuing to produce data on malaria transmission , and has led to additional projects on other tropical diseases .
Meshnick was diagnosed with cancer in 2019 .
In May this year , colleagues and mentees arranged a virtual tribute to him in which they celebrated his contributions to epidemiology , his many international collaborations , and his dedication to teaching and mentoring the next generation of infectious disease scientists .
Speaking after the tribute @ @ @ @ @ @ @ for arranging the celebration and “ for creating such a wonderful collaborative and nurturing environment at UNC.
” Addressing his trainees , he added , “ it was my honor and my privilege to be your mentor .
I just feel really lucky for having done that.
” Meshnick is survived by his wife , Mary McKinney , and four children .

“Steve was remarkable in every possible way,” Myron Cohen, director of the Institute for Global Health and Infectious Diseases at UNC, says in a statement . “He was always excited about science...
A leading researcher on the mechanisms of action of antimalarial drugs such as artemisinin, Meshnick developed long-lasting scientific connections to the Democratic Republic of Congo (DRC), Malawi, Thailand, and Cambodia, among other countries. He helped to conduct training and build research capacity in these countries alongside his work at the University of North Carolina (UNC), Chapel Hill, where he was based for the last two decades.
pidemiologist Steve Meshnick, whose work on malaria and other tropical diseases left a lasting effect on public health research in multiple African and Asian countries, died from cancer last week (August 5). He was 68.
Born in New York City in 1952, Meshnick completed an undergraduate degree in biochemistry at Columbia University in 1972, before earning graduate degrees in medical biochemistry at Rockefeller University and medicine at Cornell University in 1978 and 1979, respectively. After a number of appointments in the US and abroad—including one as a visiting scientist at the International Laboratory for Research in Animal Diseases in Nairobi in 1978—Meshnick took up a faculty position in 1992 at the University of Michigan, where he would remain for nearly 10 years before moving to UNC.
Over the course of his four-decade career, Meshnick published more than 350 scientific articles, at least 100 of which focused on drug resistance in tropical pathogens. In particular, he was a proponent of using molecular and genetic tools in epidemiology, becoming an early adopter of techniques such as real-time PCR for detecting infections with Plasmodium falciparum, the parasite that causes malaria.
Some of his best known work was on the mechanisms of action of the antimalarial drug artemisinin. In a number of papers published in the 1990s, he and colleagues in the US and China revealed how the drug reacts with proteins and other compounds in Plasmodium and reported that it binds to several different parasite proteins—a conclusion complemented by recent findings from other researchers that the drug blocks multiple cellular pathways in the parasite.
Throughout his career, Meshnick formed sustained relationships with scientists in other countries. In the early 2000s, he established a partnership with researchers in the DRC, and recently committed funds he received from a UNC award for mentoring to support the doctoral studies of a DRC-based collaborator. An epidemiological project he helped establish in Kinshasa that has now recruited more than 1,600 participants is continuing to produce data on malaria transmission, and has led to additional projects on other tropical diseases.
Meshnick was diagnosed with cancer in 2019. In May this year, colleagues and mentees arranged a virtual tribute to him in which they celebrated his contributions to epidemiology, his many international collaborations, and his dedication to teaching and mentoring the next generation of infectious disease scientists.
Speaking after the tribute, Meshnick thanked his colleagues and friends for arranging the celebration and “for creating such a wonderful collaborative and nurturing environment at UNC.” Addressing his trainees, he added, “it was my honor and my privilege to be your mentor. I just feel really lucky for having done that.”
Meshnick is survived by his wife, Mary McKinney, and four children.


thescientist--2020-08-13--Advances in Nucleic Acid Sequencing

Advances in Nucleic Acid Sequencing

Nucleic acid sequencing enables researchers to understand life at a level of detail that was once unimaginable .
The field @ @ @ @ @ researchers regularly developing new methods for advanced exploration .
Download this eBook from The Scientist @ @ @ @ @ learn about three new sequencing methods .
• Full-length poly ( A ) and mRNA @ @ @ @ @ that polyadenylation may be a misnomer

Nucleic acid sequencing enables researchers to understand life at a level of detail that was once unimaginable. The field continues to progress, with researchers regularly developing new methods for advanced exploration.
Download this eBook from The Scientist's Creative Services team to learn about three new sequencing methods.


thescientist--2020-08-13--Reduce Your Laboratory's Carbon Footprint

Labs consume a large amount of energy due to their energy-intensive equipment , continual operations , outside air requirements , @ @ @ @ @ While labs around the world have made sincere efforts to reduce their carbon footprints and @ @ @ @ @ recent global response to the coronavirus pandemic has highlighted how changing behaviors and adopting new @ @ @ @ @ .
Download this article from Stirling Ultracold to learn • How to reduce your laboratory @ @ @ @ @ equipment uses the most energy

Labs consume a large amount of energy due to their energy-intensive equipment, continual operations, outside air requirements, and high airflow rates. While labs around the world have made sincere efforts to reduce their carbon footprints and combat climate change, the recent global response to the coronavirus pandemic has highlighted how changing behaviors and adopting new technologies profoundly affects the environment.
Download this article from Stirling Ultracold to learn


thescientist--2020-08-14--Mark Konishi, Pioneer of Studying Behavior’s Neural Basis, Dies

Masakazu “ Mark ” Konishi , renowned for his research on the neuroscience of owl hunting and birdsong , died July 23 .
He was 87 .
Konishi , who conducted his work in two separate labs at Caltech , discovered that barn owls ’ hearing is essential for them to home in on prey and that young male songbirds learn their tunes from a “ tutor , ” typically their father , and then use those tunes to develop their own songs .
“ Mark picked his scientific direction based on his curiosity , ” Rockefeller University neurobiologist Fernando @ @ @ @ @ @ @ and a leader in birdsong neurobiology himself , tells The Scientist .
“ He was not an imitator.
” Konishi was born in Kyoto , Japan , on February 17 , 1933 .
Despite his father only having a few years of schooling and his mother having none , Konishi ’ s parents , silk weavers , made sure their son had more opportunities than they did .
Konishi ’ s father read to him before he learned to read in school and a neighbor helped him with simple mathematics .
Around the @ @ @ @ @ @ @ embroiled in the Pacific theater of World War II , and while Kyoto was spared from bombing by the US military , food was scarce .
Konishi grew edible plants in his backyard and his pet rabbits , which he fattened up on weeds , eventually “ became important sources of proteins , ” he wrote in his 2008 autobiography for the Society for Neuroscience .
After the war ended , his relationship with animals changed , as “ insects , fish , birds , rabbits , and dogs , ” became his @ @ @ @ @ @ @ , he wrote , when a teacher showed him two spiders fighting after the arachnids met on a stick .
“ I was so happy to see that even our teacher ( God for us ) played like me.
” Because Konishi ’ s parents did not have much education , no role model existed for him to continue to go to school after his first few years .
Relatives even suggested he forgo additional schooling .
Neither Konishi nor his parents took that advice .
He followed a friend to a private @ @ @ @ @ @ @ help of a family acquaintance , later transferred to a newly opened public high school .
There , hearing his biology teacher ’ s stories of Hokkaido University in Sapporo , Konishi decided he wanted to go to college and so he traveled for the first time to Tokyo to take the entrance exams required for admission .
He passed and was admitted .
At Hokkaido University , Konishi became intrigued with neurophysiology and learned of Nikolaas Tinbergen ’ s studies on animal behavior .
This field of study was called ethology , @ @ @ @ @ @ @ In ethology , “ one gets paid and praised for fooling animals with dummies , ” Konishi wrote in his autobiography .
“ I was already doing it as a child.
” Such fascination with the way animals act led Konishi to design an experiment on great reed warblers , specifically , probing a single territorial male ’ s response to tape-playback of his own song .
He also studied cuckoos ’ use of brood parasitism , because they laid their eggs in the warblers ’ nests .
The brains of owls and @ @ @ @ @ @ @ and master ’ s degrees at Hokkaido , then earned a Fulbright travel fellowship to cross the Pacific to come to the US .
On the ocean voyage , Konishi decided to change his name to Mark , as many of the letters were similar to his Japanese name .
He began his PhD at the University of California , Berkeley , in 1958 , ultimately joining the lab of ethologist Peter Marler .
There , Konishi expanded on his experimentation with songbirds , deafening them to see how the inability to hear @ @ @ @ @ @ @ showed that hearing the song of a tutor , typically the bird ’ s father , was essential for the youngsters to learn to sing their complex songs .
In Marler ’ s lab , Konishi also met Nottebohm , who joined the lab as an undergraduate .
“ Mark and I became fast friends and that friendship lasted the remainder of our lives , ” Nottebohm says .
“ With Mark and Peter Marler , I was the third Musketeer in that little group that was interested in figuring out how vocal @ @ @ @ @ @ @ a critical mass to talk about vocal learning and imagine experiments to study it.
” After completing his PhD in Marler ’ s lab in 1963 , Konishi moved to Germany , undertaking a year-long postdoc at the University of Tubingen .
He did a second postdoc at the Max Planck Institute , spent a year at the University of Wisconsin , then moved to Princeton University in 1966 when he began studying owl behavior as he continued his work on songbirds .
Konishi was recruited to Caltech in 1975 .
At Caltech @ @ @ @ @ @ @ of how owls hunt .
“ Mark and his protégés demonstrated that the brains of barn owls possess a three-dimensional map of space constructed from auditory information , thus showing that owls can ‘ see ’ the world with their ears , ” Caltech bioengineer and neuroscientist Michael Dickinson says in a university memorial .
“ This research helped establish how all brains , including ours , use sensory information to construct elaborate maps of the environment.
” Konishi ’ s research also revealed more on how young male songbirds learn their tutors @ @ @ @ @ @ @ fine-tuning the melodies to attract females .
“ This research helped establish songbirds as important models for understanding motor learning and language acquisition , ” Dickinson says .
Along with his research , Konishi took great interest in mentoring students and advising colleagues .
“ Mark ’ s laboratory was characterized by an emphasis on complete freedom , and that spawned independence and creativity , ” Caltech cognitive neuroscientist Ralph Adolphs , who was a PhD student of Konishi , says in the memorial .
“ When I started as a graduate student @ @ @ @ @ @ @ knew nothing .
When I came back as faculty to Caltech in 2004 , I felt I knew how to run things , and it was because of my experience with Mark ’ s paramount emphasis on ideas and pursuit of the big open questions.
” Konishi was a member of the American Academy of Arts and Sciences and the National Academy of Sciences and his work earned him a long list of awards , notably , the International Prize for Biology ( 1990 ) , the Gerard Prize from the Society for @ @ @ @ @ @ @ Spencer Lashley Award from the American Philosophical Society ( 2004 ) , and the Peter and Patricia Gruber Prize in Neuroscience from the Society for Neuroscience ( 2005 ) .

Konishi was born in Kyoto, Japan, on February 17, 1933. Despite his father only having a few years of schooling and his mother having none, Konishi’s parents, silk weavers, made sure their son had more opportunities than they did. Konishi’s father read...
Masakazu “Mark” Konishi, renowned for his research on the neuroscience of owl hunting and birdsong, died July 23. He was 87. Konishi, who conducted his work in two separate labs at Caltech, discovered that barn owls’ hearing is essential for them to home in on prey and that young male songbirds learn their tunes from a “tutor,” typically their father, and then use those tunes to develop their own songs.
Around the time Konishi turned eight, Japan became embroiled in the Pacific theater of World War II, and while Kyoto was spared from bombing by the US military, food was scarce. Konishi grew edible plants in his backyard and his pet rabbits, which he fattened up on weeds, eventually “became important sources of proteins,” he wrote in his 2008 autobiography for the Society for Neuroscience. After the war ended, his relationship with animals changed, as “insects, fish, birds, rabbits, and dogs,” became his best playmates. Konishi was in awe, he wrote, when a teacher showed him two spiders fighting after the arachnids met on a stick. “I was so happy to see that even our teacher (God for us) played like me.”
Because Konishi’s parents did not have much education, no role model existed for him to continue to go to school after his first few years. Relatives even suggested he forgo additional schooling. Neither Konishi nor his parents took that advice. He followed a friend to a private middle school, and then with the help of a family acquaintance, later transferred to a newly opened public high school. There, hearing his biology teacher’s stories of Hokkaido University in Sapporo, Konishi decided he wanted to go to college and so he traveled for the first time to Tokyo to take the entrance exams required for admission. He passed and was admitted.
At Hokkaido University, Konishi became intrigued with neurophysiology and learned of Nikolaas Tinbergen’s studies on animal behavior. This field of study was called ethology, and Konishi became captivated by it. In ethology, “one gets paid and praised for fooling animals with dummies,” Konishi wrote in his autobiography. “I was already doing it as a child.” Such fascination with the way animals act led Konishi to design an experiment on great reed warblers, specifically, probing a single territorial male’s response to tape-playback of his own song. He also studied cuckoos’ use of brood parasitism, because they laid their eggs in the warblers’ nests.
The brains of owls and songbirds
Konishi completed his bachelor’s and master’s degrees at Hokkaido, then earned a Fulbright travel fellowship to cross the Pacific to come to the US. On the ocean voyage, Konishi decided to change his name to Mark, as many of the letters were similar to his Japanese name. He began his PhD at the University of California, Berkeley, in 1958, ultimately joining the lab of ethologist Peter Marler. There, Konishi expanded on his experimentation with songbirds, deafening them to see how the inability to hear would affect their songs. His work showed that hearing the song of a tutor, typically the bird’s father, was essential for the youngsters to learn to sing their complex songs. In Marler’s lab, Konishi also met Nottebohm, who joined the lab as an undergraduate.
“Mark and I became fast friends and that friendship lasted the remainder of our lives,” Nottebohm says. “With Mark and Peter Marler, I was the third Musketeer in that little group that was interested in figuring out how vocal learning happened. It provided us with a critical mass to talk about vocal learning and imagine experiments to study it.”
After completing his PhD in Marler’s lab in 1963, Konishi moved to Germany, undertaking a year-long postdoc at the University of Tubingen. He did a second postdoc at the Max Planck Institute, spent a year at the University of Wisconsin, then moved to Princeton University in 1966 when he began studying owl behavior as he continued his work on songbirds. Konishi was recruited to Caltech in 1975.
At Caltech, Konishi began to investigate the intricacies of how owls hunt. “Mark and his protégés demonstrated that the brains of barn owls possess a three-dimensional map of space constructed from auditory information, thus showing that owls can ‘see’ the world with their ears,” Caltech bioengineer and neuroscientist Michael Dickinson says in a university memorial. “This research helped establish how all brains, including ours, use sensory information to construct elaborate maps of the environment.”
Konishi’s research also revealed more on how young male songbirds learn their tutors’ songs, then practice them, fine-tuning the melodies to attract females. “This research helped establish songbirds as important models for understanding motor learning and language acquisition,” Dickinson says.
Along with his research, Konishi took great interest in mentoring students and advising colleagues. “Mark’s laboratory was characterized by an emphasis on complete freedom, and that spawned independence and creativity,” Caltech cognitive neuroscientist Ralph Adolphs, who was a PhD student of Konishi, says in the memorial. “When I started as a graduate student, I was terrified, since I knew nothing. When I came back as faculty to Caltech in 2004, I felt I knew how to run things, and it was because of my experience with Mark’s paramount emphasis on ideas and pursuit of the big open questions.”
Konishi was a member of the American Academy of Arts and Sciences and the National Academy of Sciences and his work earned him a long list of awards, notably, the International Prize for Biology (1990), the Gerard Prize from the Society for Neuroscience (2004), the Karl Spencer Lashley Award from the American Philosophical Society (2004), and the Peter and Patricia Gruber Prize in Neuroscience from the Society for Neuroscience (2005).


thescientist--2020-08-14--Doctors Forge Ahead with Plasma for COVID-19, Benefits Uncertain

Beginning early on in the coronavirus pandemic , some researchers looked to experiences of past outbreaks for lessons , proposing that some patients might be saved by a decidedly old-fashioned remedy : plasma taken from people who ’ d recovered from the disease in infused into patients .
The idea is that such plasma contains antibodies against SARS-CoV-2 that can give patients ’ immune systems a boost in fighting the disease .
The approach caught on .
Presently , about 1,500 patients a day are receiving this treatment in the US , Buzzfeed reports—but convalescent plasma ’ s very popularity @ @ @ @ @ @ @ answers on whether the remedy really works , and for whom .
“ Without a randomized control trial , it ’ s very difficult to be certain that what you have is meaningful , ” epidemiologist W. Ian Lipkin of Columbia University tells The New York Times .
Lipkin had been conducting such a trial , in which patients are randomly assigned to receive either plasma or a placebo , but the outbreak in New York died down before the trial had enrolled enough participants .
Lipkin says he looked for partners in @ @ @ @ @ @ @ continue the study , but had a hard time finding them because patients and their doctors are reluctant to participate knowing they might receive the placebo .
Since early April , many patients have been receiving plasma outside of clinical trials through a Food and Drug Administration ( FDA ) –sanctioned program run by the Mayo Clinic .
That initiative had published a preprint last month indicating that the plasma treatment is safe , and this week it put out further results on 35,322 treated patients indicating that those who received infusions with @ @ @ @ @ @ @ those who received the treatment earlier in their illness , were more likely to survive than patients who received less–antibody-rich plasma or received it later .
But the Mayo study does not include a control group , and randomized controlled trials that have been completed on convalescent plasma for COVID-19 have been much smaller .
In one study published in JAMA in June , researchers based in China reported that they did not find a statistically significant difference in recovery within 28 days for patients who received the treatment , but they had @ @ @ @ @ @ @ the trial and they wrote in their report that it “ may have been underpowered to detect a clinically important difference.
” See “ FDA to Allow for Plasma Therapy for COVID-19 Patients ” Trials in the US have similarly stalled due to an inability to recruit enough patients , the Times reports , and meanwhile , its sources say that the FDA is preparing an emergency use authorization for convalescent plasma that could further expand its use .
The Mayo Clinic ’ s new study “ raises the question of what strength @ @ @ @ @ @ @ a pandemic , ” says Harlan Krumholz , director of the Center for Outcomes Research and Evaluation at Yale New Haven Hospital , in comments to STAT .
“ The problem is we have yet to resolve what is sufficient evidence to change the treatment paradigm.
” Even if convalescent plasma has benefit , it “ was never intended to be the final treatment for a disease , ” infectious disease expert Nicole Bouvier of the Icahn School of Medicine at Mount Sinai who is involved with the Mayo study tells BuzzFeed .
@ @ @ @ @ @ @ work on making other therapeutics .
”

“Without a randomized control trial, it’s very difficult to be certain that what you have is meaningful,” epidemiologist W. Ian Lipkin of Columbia University tells The New York Times . Lipkin had been conducting such a trial, in which patients are...
Beginning early on in the coronavirus pandemic, some researchers looked to experiences of past outbreaks for lessons, proposing that some patients might be saved by a decidedly old-fashioned remedy: plasma taken from people who’d recovered from the disease in infused into patients. The idea is that such plasma contains antibodies against SARS-CoV-2 that can give patients’ immune systems a boost in fighting the disease. The approach caught on. Presently, about 1,500 patients a day are receiving this treatment in the US, Buzzfeed reports—but convalescent plasma’s very popularity is making it difficult to get solid answers on whether the remedy really works, and for whom.
Since early April, many patients have been receiving plasma outside of clinical trials through a Food and Drug Administration (FDA)–sanctioned program run by the Mayo Clinic. That initiative had published a preprint last month indicating that the plasma treatment is safe, and this week it put out further results on 35,322 treated patients indicating that those who received infusions with a greater concentration of antibodies, and those who received the treatment earlier in their illness, were more likely to survive than patients who received less–antibody-rich plasma or received it later.
But the Mayo study does not include a control group, and randomized controlled trials that have been completed on convalescent plasma for COVID-19 have been much smaller. In one study published in JAMA in June, researchers based in China reported that they did not find a statistically significant difference in recovery within 28 days for patients who received the treatment, but they had only managed to enroll 103 patients in the trial and they wrote in their report that it “may have been underpowered to detect a clinically important difference.”
Trials in the US have similarly stalled due to an inability to recruit enough patients, the Times reports, and meanwhile, its sources say that the FDA is preparing an emergency use authorization for convalescent plasma that could further expand its use.
The Mayo Clinic’s new study “raises the question of what strength of evidence is necessary to treat during a pandemic,” says Harlan Krumholz, director of the Center for Outcomes Research and Evaluation at Yale New Haven Hospital, in comments to STAT. “The problem is we have yet to resolve what is sufficient evidence to change the treatment paradigm.”
Even if convalescent plasma has benefit, it “was never intended to be the final treatment for a disease,” infectious disease expert Nicole Bouvier of the Icahn School of Medicine at Mount Sinai who is involved with the Mayo study tells BuzzFeed. “It gives us more time to work on making other therapeutics.”


thescientist--2020-08-14--Book Excerpt from The State of Science

Book Excerpt from The State of Science

We all need experts .
Scientists will be happy to tell you that journalists , consumers , and policy makers don ’ t understand science and need expert advice .
But they themselves struggle to see that they also need input from experts .
We scientists need to learn how to increase the diversity of our field , consider the ethics of what we are doing , and reach out to nonscientists and explain our work .
The knowledge gap between experts ( be they scientists , medical doctors , or economists ) and nonexperts is increasing , and perversely @ @ @ @ @ @ @ .
This is due in part to the fact that we often have a misguided overconfidence in our knowledge , something Leonid Rozenblit and Frank Keil , psychologists at Yale University , termed the illusion of explanatory depth .
According to them , “ most people feel they understand the world with far greater detail , coherence , and depth than they really do ” and consequently have less use for experts than they should .
A little more than a century ago , Richard Burdon Haldane wrote a report for the British @ @ @ @ @ @ @ politician , advocated putting scientists in charge of deciding who should receive government research funding and that politicians should stay out of funding deliberations and when making science policy should listen to the advice of experts .
His ideas would come to be known as the Haldane Principle , and it would take the upheaval of the Second World War for them to take root .
In World War II , scientific technologies such as radar and the atomic bomb were central to the Allies ’ victory .
Following the war , scientists @ @ @ @ @ @ @ and politics , arguing that if science could win wars , it could also help to hold peace .
They were successful , and many nations adopted the Haldane Principle .
By 2015 , U.S. federal agencies had about 1,000 advisory panels relying on the expertise of roughly 60,000 members .
They advised government agencies on everything from foodborne illness , to drug safety , to air and water pollution .
They were there to provide fact-based advice and evidence .
After all , no one can reasonably expect our elected representatives to @ @ @ @ @ @ @ rely on the expertise of professionals .
However , recently that approach has changed .
On June 14 , 2019 , President Trump signed an executive order to reduce all advisory boards by one-third , a telling move that will have long-term consequences .
In a comment published in Nature in 2018 , Ehsan Masood worries that an expanding global network of populist political movements is deriding independent scholarship and erasing the protections granted by the Haldane Principle .
Masood calls out Trump and the UK Brexiteers and worries , “ Today , @ @ @ @ @ @ @ to Rio de Janeiro , a parade of authoritarian leaders is advancing policies that fly in the face of evidence—on energy , emissions , the environment , economics , immigration and more .
Worse , these leaders are demanding that academics march to the beat of their drums.
” Scientists are no longer advising politicians , and politics is driving science policy .
This is particularly true for the Trump administration , which in making its science policy has been much more interested in soliciting advice from industrialists than scientists .
It has @ @ @ @ @ @ @ It has at best an apathetic stance toward science and at worst is actively hostile , particularly toward the environmental sciences .
In the first year of the Trump administration , nearly two-thirds of the science advisory boards met less often than required by their charters , and they met less frequently than in any other administration .
From the beginning , the administration has tried to reduce the staff and budget of the Environmental Protection Agency ( EPA ) and to undermine its use of science in policy making .
As a @ @ @ @ @ @ @ in enforcement of the Clean Air Act and Clean Water Act in nearly all regions of the United States .
And environmental policies have been amended on advice from industrial advisers against the advice of the scientific community .
There are so many instances of the Trump administration attempting to scale back or wholly eliminate federal climate mitigation and adaptation guidelines that I can ’ t catalog them all .
The Columbia Law School ’ s Sabin Center for Climate Change Law maintains the Climate Deregulation Tracker .
In July 2019 , Science @ @ @ @ @ @ @ Drug Administration ] enforcement actions plummet under Trump.
” The FDA is one of the nation ’ s critical watchdogs .
Its warning letters , its primary tool for keeping dangerous and ineffective pharmaceuticals off the market , have dropped by a third .
The agency has been particularly lax in its oversight of medical devices , with the Center for Devices and Radiological Health sending out two- thirds fewer warnings .
The danger in all these attacks on science is that it is nearly impossible to keep track of them .
We @ @ @ @ @ @ @ science and environmental deregulation that we are overwhelmed , and some pass us by .
Philip B. Duffy , president of the Woods Hole Research Center and a National Academy of Sciences panelist , who reviewed the government ’ s most recent climate assessment , told The New York Times , “ What we have here is a pretty blatant attempt to politicize the science—to push the science in a direction that ’ s consistent with their politics.
” He added , “ It reminds me of the Soviet Union.
” That is @ @ @ @ @ @ @ an impartial scientist .
The Trump administration is certainly not the first administration to change the scientific policies of its predecessors , as is its right .
However , it is the first to systematically chip away at large portions of science-related policies and legislation without consulting scientists , while at the same time undermining the scientific process to discredit climate scientists and public health researchers .
It is difficult to accept that Trump , whose errors in science are so crude and blatant , can undermine science .
How can someone who @ @ @ @ @ @ @ cancer command more respect than the combined thinking of thousands of scientists ?
But in today ’ s politics , anything is possible , and people are happy to accept his inane utterances over the well-proven scientific method .
To me , nothing demonstrates the intention to influence the way we think about science more than the fact that employees of the Centers for Disease Control are now not allowed to use the words “ evidence-based , ” “ science- based , ” and “ fetus , ” and that staff at the @ @ @ @ @ @ @ told never to use the phrase “ climate change ” ; instead they have to say “ weather extremes ” and replace “ adaptation ” with “ resilience.
” Soviet indeed .
The devaluation of science by the Trump administration has had some unfortunate consequences .
John Holdren , who was President Obama ’ s science adviser and may be slightly biased , has said , “ Trump , along with his picks to lead major scientific agencies , act as talent repellents , because they appear to know little and care less @ @ @ @ @ @ @ and technology in shaping public policy.
” It is important to remember that Trump ’ s disregard of science and the environment plays well with a substantial fraction of the U.S. population and doesn ’ t reflect just the opinion of one person .
A significant segment of the population resents science .
The most obvious future consequences of the undermining of the scientific process and the marginalization of science , particularly public health and environmental science , by the Trump administration are difficulties in dealing with climate change , the degradation of @ @ @ @ @ @ @ in the competitiveness of U.S. science and technology .
Excerpted with permission from The State of Science : What the Future Holds and the Scientists Making it Happen by Marc Zimmer ( Prometheus , July 2020 ) .

The knowledge gap between experts (be they scientists, medical doctors, or economists) and nonexperts is increasing, and perversely our reliance on these experts is decreasing. This is due in part to the fact that we often have a misguided overconfidence in our knowledge, something Leonid Rozenblit and Frank Keil, psychologists at Yale University, termed the illusion of explanatory depth. According to them, “most people feel they understand the world with...
We all need experts. Scientists will be happy to tell you that journalists, consumers, and policy makers don’t understand science and need expert advice. But they themselves struggle to see that they also need input from experts. We scientists need to learn how to increase the diversity of our field, consider the ethics of what we are doing, and reach out to nonscientists and explain our work.
A little more than a century ago, Richard Burdon Haldane wrote a report for the British Parliament in which he, a career politician, advocated putting scientists in charge of deciding who should receive government research funding and that politicians should stay out of funding deliberations and when making science policy should listen to the advice of experts. His ideas would come to be known as the Haldane Principle, and it would take the upheaval of the Second World War for them to take root.
In World War II, scientific technologies such as radar and the atomic bomb were central to the Allies’ victory. Following the war, scientists advocated for a separation between science policy and politics, arguing that if science could win wars, it could also help to hold peace. They were successful, and many nations adopted the Haldane Principle. By 2015, U.S. federal agencies had about 1,000 advisory panels relying on the expertise of roughly 60,000 members. They advised government agencies on everything from foodborne illness, to drug safety, to air and water pollution. They were there to provide fact-based advice and evidence. After all, no one can reasonably expect our elected representatives to master every topic; they have to rely on the expertise of professionals.
However, recently that approach has changed. On June 14, 2019, President Trump signed an executive order to reduce all advisory boards by one-third, a telling move that will have long-term consequences. In a comment published in Nature in 2018, Ehsan Masood worries that an expanding global network of populist political movements is deriding independent scholarship and erasing the protections granted by the Haldane Principle. Masood calls out Trump and the UK Brexiteers and worries, “Today, from Istanbul to Islamabad, from Rome to Rio de Janeiro, a parade of authoritarian leaders is advancing policies that fly in the face of evidence—on energy, emissions, the environment, economics, immigration and more. Worse, these leaders are demanding that academics march to the beat of their drums.” Scientists are no longer advising politicians, and politics is driving science policy.
This is particularly true for the Trump administration, which in making its science policy has been much more interested in soliciting advice from industrialists than scientists. It has scant regard for the Haldane Principle. It has at best an apathetic stance toward science and at worst is actively hostile, particularly toward the environmental sciences. In the first year of the Trump administration, nearly two-thirds of the science advisory boards met less often than required by their charters, and they met less frequently than in any other administration. From the beginning, the administration has tried to reduce the staff and budget of the Environmental Protection Agency (EPA) and to undermine its use of science in policy making. As a consequence, there have been steep drops in enforcement of the Clean Air Act and Clean Water Act in nearly all regions of the United States. And environmental policies have been amended on advice from industrial advisers against the advice of the scientific community. There are so many instances of the Trump administration attempting to scale back or wholly eliminate federal climate mitigation and adaptation guidelines that I can’t catalog them all. The Columbia Law School’s Sabin Center for Climate Change Law maintains the Climate Deregulation Tracker.
In July 2019, Science reported that “FDA [Food and Drug Administration] enforcement actions plummet under Trump.” The FDA is one of the nation’s critical watchdogs. Its warning letters, its primary tool for keeping dangerous and ineffective pharmaceuticals off the market, have dropped by a third. The agency has been particularly lax in its oversight of medical devices, with the Center for Devices and Radiological Health sending out two- thirds fewer warnings. The danger in all these attacks on science is that it is nearly impossible to keep track of them. We are so bombarded with blatant misrepresentations of science and environmental deregulation that we are overwhelmed, and some pass us by.
Philip B. Duffy, president of the Woods Hole Research Center and a National Academy of Sciences panelist, who reviewed the government’s most recent climate assessment, told The New York Times, “What we have here is a pretty blatant attempt to politicize the science—to push the science in a direction that’s consistent with their politics.” He added, “It reminds me of the Soviet Union.” That is not what we want to hear from an impartial scientist. The Trump administration is certainly not the first administration to change the scientific policies of its predecessors, as is its right. However, it is the first to systematically chip away at large portions of science-related policies and legislation without consulting scientists, while at the same time undermining the scientific process to discredit climate scientists and public health researchers. It is difficult to accept that Trump, whose errors in science are so crude and blatant, can undermine science. How can someone who says that the noise windmills make causes cancer command more respect than the combined thinking of thousands of scientists? But in today’s politics, anything is possible, and people are happy to accept his inane utterances over the well-proven scientific method.
To me, nothing demonstrates the intention to influence the way we think about science more than the fact that employees of the Centers for Disease Control are now not allowed to use the words “evidence-based,” “science- based,” and “fetus,” and that staff at the United States Department of Agriculture have been told never to use the phrase “climate change”; instead they have to say “weather extremes” and replace “adaptation” with “resilience.” Soviet indeed. The devaluation of science by the Trump administration has had some unfortunate consequences. John Holdren, who was President Obama’s science adviser and may be slightly biased, has said, “Trump, along with his picks to lead major scientific agencies, act as talent repellents, because they appear to know little and care less about the value of insights from science and technology in shaping public policy.”
It is important to remember that Trump’s disregard of science and the environment plays well with a substantial fraction of the U.S. population and doesn’t reflect just the opinion of one person. A significant segment of the population resents science.
The most obvious future consequences of the undermining of the scientific process and the marginalization of science, particularly public health and environmental science, by the Trump administration are difficulties in dealing with climate change, the degradation of the U.S. environment, and a decline in the competitiveness of U.S. science and technology.
Excerpted with permission from The State of Science: What the Future Holds and the Scientists Making it Happen by Marc Zimmer (Prometheus, July 2020).