Image of a single suspended atom nabs science photography prize

A university student named David Nadlinger has won the top prize in a science photography contest held by UK’s Engineering and Physical Sciences Research Council after capturing a photo of a single atom.

The photo, titled “Single Atom in an Ion Trap” shows a single atom suspended in midair. It was captured using a standard DSLR camera and shows the tiniest speck of a positively charged strontium atom. The atom’s place is being held by an electric field created by two metal electrodes. When illuminated with a blue-violet laser, as shown in the photo, the atom absorbed and reemits enough light to make it so an ordinary camera can capture it with a long exposure. For perspective on just how small this entire scene is, the distance between the ion and the electrode tips on either side is about two millimeters.

Nadlinger is a PhD candidate at the University of Oxford, and he traps atoms for his quantum computing research. He captured the image because “the idea of being able to see a single atom with the naked eye had struck me as a wonderfully direct and visceral bridge between the miniscule quantum world and our macroscopic reality. A back-of-the-envelope calculation showed the numbers to be on my side, and when I set off to the lab with camera and tripods one quiet Sunday afternoon, I was rewarded with this particular picture of a small, pale blue dot.”

Other photographs that took home prizes in individual categories included a robot taking a selfie, a spherical soap bubble that shows fluid instability patterns, and a volunteer wearing an Electroencephalography (EEG) headset to record brain activity.

AI is helping seismologists detect earthquakes they’d otherwise miss

Oklahoma never used to be known for its earthquakes. Before 2009, the state had roughly two quakes of magnitude three and above each year. (Magnitude three is when things shake on the shelf, but before houses start getting damaged.) In 2015, this tally rocketed to more than 900, though it’s calmed since, falling to 304 last year.

This sudden increase is thought to be caused by the disposal of wastewater by the state’s booming fracking industry, and it’s caught seismologists off-guard. As a historically quake-free area, Oklahoma doesn’t have enough equipment to detect and locate all of these quakes, making it hard to investigate their root cause. “There are no major faults in Oklahoma so it’s just not something we would expect,” Thibaut Perol, a deep learning researcher who’s worked on this problem, tells The Verge. “And to understand what’s happening, we need a big, big catalogue of earthquakes.”

The solution proposed by Perol and his colleagues from Harvard University’s engineering and earth sciences departments is to use artificial intelligence to amplify the sensitivity of the state’s earthquake detectors, otherwise known as seismographs. In a paper published today in the journal Science Advances, they show how effective this technique is — capable of detecting 17 times more earthquakes than older methods in a fraction of the time.

The method is similar to the voice detection software used by digital assistants like Alexa and Siri, explains Perol. It’s all about uncovering the signal hidden in the noise. With Alexa, that means listening out for your voice commands while ignoring the background sound of your home. And for seismographs, it means cancelling out the normal geological rumblings of the Earth (what’s known as “ambient seismic noise”) to spot the earthquakes that might be very small or far away. This way, scientists in Oklahoma can get more out of the data they already have.

To make this happen, Perol and his colleagues trained a convolutional neural network to recognize background noise, feeding it data from seismically quiet areas, like pre-fracking era Oklahoma and the geological dead-zone of Wisconsin. (The state has only really had one significant earthquake, and that was in 1947.) As with all neural networks, the software examines this input and learns to pick out common patterns. Once it knows what ambient rumblings sound like, it can remove these from the data, leaving behind the tiny earthquakes that had previously been hidden — like sea shells revealed by a retreating tide. As a bonus, the neural network is even able to identify the rough whereabouts of individual quakes by matching the patterns they created with historical data where a tremor’s location was known.

“With this method we are able to detect earthquakes of magnitude zero or minus one, and these are signals you wouldn’t be able to see with a human eye,” says Perol.

William Yeck, a seismologist at the United States Geological Survey (USGS), praised the work as “compelling and novel.” Speaking to The Verge by email, he noted that the neural network would best apply to “local earthquake monitoring efforts” — as in Oklahoma — “where there are high-seismicity rates.” Yeck cautions, though, that earthquake detection is only ever going to be a part of the puzzle. “Estimations of earthquake sizes and accurate event locations are also necessary,” says Yeck. “For the very small events that this technique detects, this will be challenging.”

If this neural network can be used more widely in Oklahoma applied, says Perol, it’ll help seismologists investigate the exact cause of the state’s earthquakes. There’s even some hope that it could predict earthquakes before they occur. This could be done by looking for patterns in the data; for example, finding times when a number of small earthquakes have happened in quick succession, triggering a bigger, potentially damaging quake.

The idea of using AI to predict — not just detect — earthquakes is an exciting one, but it’s not something that the whole seismologist community is confident about. (You can watch the video below for more info.) In Oklahoma at least, prediction isn’t as pressing as detection. But with the help of Perol and his colleagues’ neural network, this important work could get a boost.

The upside of awkwardness: writer Melissa Dahl explains why we cringe, and why it can be a good thing

It’s hard to fault anyone for thinking that awkwardness is to be avoided. The familiar, sinking feeling of knowing you’ve embarrassed yourself does not rank high on the hierarchy of desirable emotions.

Still, says journalist Melissa Dahl, there is something to be gained in embracing awkwardness — and the much-hated feeling can bring us together. Dahl, a senior editor at New York Magazine’s The Cut, is the author of Cringeworthy: A Theory of Awkwardness, out today from Portfolio Books. She’s spent two years studying awkwardness, which means immersing herself in the psychological research, but also putting herself to the test by talking to strangers on the subway and reading her seventh grade diary in front of a crowd.

The Verge spoke to Dahl about how awkwardness is different from embarrassment and anxiety, what the research tells us about whether anyone is paying attention, different types of secondhand embarrassment, and what happens if we stop fearing those awkward moments.

This interview has been lightly edited for clarity.

First things first: what made you interested in writing a book about awkwardness?

It’s a feeling that’s driven me insane for most of my life, but I started thinking about it more when I did this exceedingly silly story for Science of Us. A study came out by Nicholas Epley at the University of Chicago and a lot of people were reporting on it, saying, “If you talk to strangers on the subway in the morning before work, you’ll be happier.” I read that and I was just like, that cannot be true!

So I spent a week trying it and there was something really exhilarating about purposefully putting myself in this excruciatingly awkward situation. In the end, it did make me a little happier, and a little more attuned to moments where you can connect with people in ways I didn’t expect. That’s when I started to think, “Oh, there’s something interesting here.” Plus, the subject just cracked me up. There’s an inherent hilarity here.

Author Melissa Dahl.
Photo by Celeste Sloman

Almost everyone knows what it means to feel “awkward,” but when you think about it, it can be hard to define. How is awkwardness different from embarrassment, self-consciousness, anxiety, or even fear?

I had to think deeply about how to define awkwardness when I was invited to speak at this amazing tiny little psychology conference called the Symposium of Neglected Emotions. A lot of these feelings… overlap — there’s social anxiety and embarrassment in awkwardness — but I think awkwardness is self-consciousness with this undercurrent of uncertainty. You’re really aware of how you’re coming off to the world and then there’s an ambiguity about what to do next.

Embarrassment is a huge part of it, too. But embarrassment is like when you get pantsed in high school. I don’t think we’d call that awkward.

There’s not that much research on awkwardness, specifically, and the title of your book is “a theory of awkwardness.” So what is Melissa’s grand unified theory of awkwardness?

I’ve been calling it “cringe theory,” and I think the idea came through a story I did on why we cringe at the sound of our own voices. The topic has been written about all over. It’s about how I’m hearing through the bones of my own skull, which is different from what you’re hearing. But what interested me was why does that make us cringe?

And then I got obsessed with this idea that maybe we feel awkward when the “you” you think you’re presenting to the world clashes with the way the world is actually seeing you. We like to think those two “yous” are one and the same, and sometimes they are, but sometimes they’re not. For example, if I’m feeling secondhand embarrassment for someone else, I think you could say it’s because they’re presenting themselves one way and don’t know they’re coming off another way. The psychologist Philippe Rochat at Emory called it “the irreconcilable gap” between who you think you are and who the world is seeing.

So, your theory is that awkwardness is what happens when the “front” we put on collapses. You also talk about how we put on different fronts for different people and one thing that’s hard now is that these differences are coming together like when you’re Facebook friends with your grandmother, old professors, and colleagues. How do we build a role that can stand different audiences?

I don’t know if there is an easy answer, but maybe we can try to do it in the most honest way possible, and keep in our heads that we contain multitudes. It’s just going to feel weird sometimes.

For me, I’ve been running into this when promoting my book, especially on Facebook where it’s mostly friends and family and not professional. So maybe I can think of it as, “Okay, this is my place where I am more of a friend and family member, but those people care about me and about this thing that I’ve made too. That’s part of me.” It’s not such a bad thing to be fully formed humans in the work sphere and in the friend sphere. Maybe those were always kind of artificial boundaries anyway.

In the course of research, you read a lot of papers. What surprised you? What was most useful? You mention one paper on “anxiety reappraisal,” which is about how we can tell ourselves that anxiety is actually excitement. Anything else?

Anxiety reappraisal is one that has stuck with me. I really love the spotlight effect too, which is the idea that nobody is really paying much attention to you. Of course, you have to be balanced about it. With things like entering a party late or entering a meeting late, it’s not that people aren’t noticing you doing embarrassing things, but not as many as you think. It’s not “do whatever you want” — of course sometimes people are looking at you — but not to the extent that most of us think. That’s freeing.

We’ve been mostly talking about awkwardness in small encounters, but you have chapters in your book talking about the awkwardness we feel about big topics like race and disability. What can awkwardness in those situations illuminate for us?

Normally, when we say “awkward,” we do mean those little moments of saying something stupid, but I was so interested to see it applied to these gigantic matters. I once clicked on a video series about why we’re awkward and it was a video series about racial bias, which is not what I was expecting. Then, I found this campaign in the UK called End the Awkward, which is all about how non-disabled people lose their minds over how to interact with a disabled person.

As I was developing cringe theory, this usage started to make sense. If awkward is about the gap between how you think you are and how someone else is seeing you, these excruciating moments where we want to run away become a little signal of an opportunity for us to be better. In these cases, it’s useful information when your inner idealized person is not being perceived well. It’s worth considering that other person’s perspective and put yourself in their shoes and think, “I don’t know everything, I meant to say it this way and they took it this way and maybe they’re right.” In these moments when we feel so uncomfortable, we can get a little closer to the person we want to be.

And I think sometimes a conversation will end up being awkward. It’s unavoidable and it’s fine! We’ll live.

I talked to Alison Green, from Ask a Manager, and she says, either you have to have the awkward conversation or live with the feeling that’s bothering you and there are different degrees of living with that thing.

Over the course of the book, I started experiencing awkwardness to a lesser degree. My friends would talk about their boss and I’m just like, just talk to them! And they say, no, I can’t do that. But a little awkwardness is not going to be uncomfortable and is not going to kill us. “Just step back and lighten up” is a lesson I’ve learned over and over again.

You read your seventh grade diary out loud to audition for the show Mortified and also go to Tinder Live, where people, well, use the app live and roast people’s profiles. The experiences of secondhand embarrassment were really different for you you loved Mortified but felt uncomfortable at Tinder Live. Why the different reactions?

The two shows take place in the same venue, so that was surreal — the conditions are the same, swap one thing out. And it became a really interesting way to investigate the idea of secondhand embarrassment and vicarious awkwardness. I once wrote about this study on secondhand embarrassment where they found that people who experience this also tend to be empathetic, and I just felt unbearably smug thinking, I’m such a good person and that’s why I have this strong reaction.

And these two shows accidentally showed me the differences. We talk about empathy as if it’s a synonym for kindness and compassion, and it can be, but psychologists like Philippe Rochat say it’s an automatic human reaction: I’m understanding what you’re feeling because we are social animals and that’s how we learn to get along. His thought is that you can either process through contempt or through compassion. It’s uncomfortable if you’re feeling empathy for someone who is embarrassing themselves. You can shut them out and be like, “I am not that idiot on Tinder on this big projection screen” or you can say, “that’s me, too. I’m feeling this way because I have been a version of that idiot.”

It might be too much to ask that we always do this for each other, but it became interesting to me to, as often as I can, try to process embarrassment through compassion. And Mortified is such an exercise in that. It’s hilarious and it’s a mix of self-recognition and tenderness because you can see yourself in every person up there. I didn’t make a website devoted to Leo DiCaprio in 1998, but I can definitely connect that to my absurd love for Hanson at that age.

I was not expecting to spend two years researching awkwardness and come out the other end with this real “common humanity” vibe but that show and this idea of compassionate cringing is what that led to. It’s a really nice feeling. It can help reframe the idea of awkwardness as something that everyone has experienced, so maybe I can choose not to drown in it and I can learn from it. It makes the feeling a little less isolating and is a nice way of connecting with other folks through our mutual human absurdity.

Sonic weapons probably didn’t cause mysterious diplomat illnesses in Cuba, doctors say

 

After months of rumors, doctors have published the first detailed report describing the mysterious illness that struck US diplomats stationed in Cuba. While the source of the illness is still a mystery, the doctors say they’re “pretty certain” it wasn’t a sonic weapon.

Doctors examined 21 people associated with the US embassy in Cuba, and found that their symptoms resembled those caused by brain injuries — including headaches, sleep disturbances, and mood changes. But surprisingly, none of the diplomats showed any obvious signs of head trauma, according to a paper published today in the Journal of the American Medical Association.

“This is really concussion without concussion,” says study co-author Douglas Smith, director of the University of Pennsylvania’s Center for Brain Injury and Repair, in a podcast interview. Smith and his colleagues speculate that the diplomats’ illness might be an entirely new disorder, caused by some sort of shared environmental exposure in Havana. But other scientists warn against leaping to conclusions, since there’s still a lot we don’t know.

Starting in 2016, US diplomats in Cuba began experiencing an unusual collection of symptoms including vertigo, nausea, and hearing loss. All but one of the diplomats reported that they first felt ill after hearing strange noises or feeling air pressure or vibrations in their homes or hotel rooms. This sparked fears that diplomats were being targeted by “health attacks,” although the FBI couldn’t turn up evidence that these were occurring. (A biologist contacted by the US government identified the strange sounds as insect calls, ProPublica reported today.)

By the fall of 2017, 80 people linked to the embassy had been screened for similar symptoms, and the number of victims climbed to 24 people. Doctors at the University of Pennsylvania’s Center for Brain Injury and Repair evaluated 21 of the patients, and found that most of them were experiencing headaches and trouble sleeping. Many had trouble thinking, concentrating, and focusing their eyes — symptoms that worsened after exercise. Three patients had severe hearing loss. Brain imaging didn’t turn up anything out of the ordinary. But nearly a year later, only seven of the 21 patients have been able to return to work full time, according to a JAMA news article.

There’s no known way for sound to cause such a serious assortment of symptoms, the study’s authors say. Instead, they suspect that the strange sounds the patients reported were a byproduct of whatever actually harmed them — kind of like the crack of a gunshot. The study’s authors don’t think infections, chemical exposures, or mass hysteria can explain the symptoms, either. “The simpler answer is that there’s something real here,” one of the authors says in a podcast.

Other experts, however, aren’t ready to rule out mass hysteria transmitted by word of mouth. For example, the study doesn’t clarify whether people whose illness started later on knew about the symptoms others had reported, an editorial points out. That could have made them more alert to those symptoms themselves. Also, the researchers evaluating the patients knew who the patients were — which could have biased their evaluations.

Still, today’s report is a step towards developing the diagnostic criteria that will be key to finding others experiencing the same symptoms. “This really is a public health matter and we have to be concerned that there could be other individuals out there who might have been exposed that we don’t know about,” one of the authors says. “People need to be prepared and I would say that our report is really just preliminary.”

Cuttlefish can put their camouflage abilities on autopilot to save energy

Not only can cuttlefish change the texture of their bodies to blend in with the ocean floor, new research shows that they can put this camouflage power on autopilot to save energy.

Scientists have long known that the cuttlefish — a relative of squid and octopi that lives on the ocean floor — can contract its skin and change its 3D texture into little bumps called papillae. By cutting open the cuttlefish, scientists in today’s study discovered the nerve in the body responsible for regulating these skin contractions and monitoring the creature’s efforts at camouflage. Most interestingly, the nerve can go on autopilot and “lock” the camouflage for an hour without using any energy. The results were published today in iScience, a journal published by Cell Press.

Interestingly, the nerve system that controls this autopilot power is very similar to the system that makes squid iridescent, so the scientists think they might have evolved from the same system. Next, they’re trying to find the link between these two systems and better understand the location of the neurons to figure out more mysteries of these ocean creatures.

Learning How to Be a Top-Notch Window Cleaner

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Numerous individuals employ their window cleaning done by an expert window cleaner on the grounds that the outcomes are generally so extraordinary. Lovely sparkly windows with no whirl checks or streaks simply don’t occur contrasted with when you clean them yourself. Be that as it may, with the correct information, materials and practice, you can likewise turn into a genius.

The Right Equipment and Supplies

There are just two essential things that you may need to buy from a janitorial supply house on the grounds that your retail establishment may not convey; a T-bar that is secured with a delicate sheepskin-type texture for wetting the glass and a 14″ squeegee. Squeegees come in various sizes, 4, 6, 8, 10, 12, 14, 16 and 18, yet an expert window cleaner more often than not finds the 14″ works for most windows and is anything but difficult to deal with. You may need a 6″ for little sheets in the event that you have many. Next, a microfibre fabric or tee shirt material, a container, dishwashing cleanser and bunches of dry fabrics will round out your cleaning supplies.

Beginning on your Window Cleaning

You needn’t bother with exceptional cleanser or glass cleaner unless the climate is to a great degree cool and you discover the water icing on the windows. For this situation, add a touch of liquor to your dishwater. A decent window cleaner dependably begins with upper windows in light of the fact that the dilute will run and get the base windows wet. Get your sheet wet with your T-bar dunked in your can of water. Beginning with a pleasant dry squeegee, put in the window’s upper corner and draw down. Wipe off your squeegee with a dry fabric and continue to the wet region close to of your dry zone. Whenever completed, wipe off the ledge with a fabric at that point utilize your microfibre material or tee shirt to circumvent the edges.

Issues Encountered with Window Cleaning

On the off chance that you have a window that is set apart with hard spots of earth, you may convey a glass scrubber with you. One end is dull for prodding soil and the opposite end has a dangerously sharp edge. A decent window cleaner dependably ensures that the window is wet before utilizing so as not to scratch the glass. The window cleaning will go a considerable measure simpler once you have expelled any knocks of earth on the sheet. A window cleaner that is relied upon to wash a sky facing window or a window that is too high for a standard stepping stool, need to utilize a shaft with the squeegee on the end. These windows will most likely not turn out flawless since you can’t see the squeegee.

Distinctive Types of Windows

Not a wide range of windows are this straightforward for a window more clean. There are lead/cross section, French/Georgian, Sculptured or small paned windows that can be a significant snag. You can’t utilize a squeegee on these in light of the surface, shape and size. The best thing you can do is wet with your T-bar, wipe off the vast majority of the abundance water with a fabric and sparkle with your microfibre material or tee shirt material.

The primary concern to recollect about window cleaning is to keep it straightforward. All the favor substance based items on the planet won’t give you a superior employment or improve you a window cleaner than plain cleanser and water. The rest is rehearse.

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Geologists Return from Expedition to Chicxulub Impact Crater

The Chicxulub crater is the only well-preserved peak-ring crater on Earth and linked to the Cretaceous-Tertiary mass extinction, an event 65 million years ago that wiped out the dinosaurs as well as nearly 50% of all the world’s species. For the first time, geologists have drilled into the peak ring of this crater in the International Ocean Discovery Program and International Continental Scientific Drilling Program (IODP-ICDP) Expedition 364.

This painting depicts an asteroid slamming into tropical, shallow seas of the sulfur-rich Yucatan Peninsula in what is today southeast Mexico. The aftermath of this immense asteroid collision, which occurred approximately 65 million years ago, is believed to have caused the extinction of the dinosaurs and many other species on Earth. Shown in this painting are pterodactyls, flying reptiles with wingspans of up to 50 feet, gliding above low tropical clouds. Image credit: Donald E. Davis / NASA.

This painting depicts an asteroid slamming into tropical, shallow seas of the sulfur-rich Yucatan Peninsula in what is today southeast Mexico. The aftermath of this immense asteroid collision, which occurred approximately 65 million years ago, is believed to have caused the extinction of the dinosaurs and many other species on Earth. Shown in this painting are pterodactyls, flying reptiles with wingspans of up to 50 feet, gliding above low tropical clouds. Image credit: Donald E. Davis / NASA.

The Cretaceous-Tertiary mass extinction occurred at the same time that a 10-km-diameter asteroid, dubbed Chicxulub, hit our planet in what is now the Yucatán Peninsula. The collision would have triggered earthquakes, tsunamis, and even volcanic eruptions.

The impact, its catastrophic effects, and its aftermath have engrossed researchers and the public alike since it was first discovered.

In spring 2016, an international team of geologists on the IODP-ICDP Expedition 364 drilled into the Chicxulub crater off the coast of Mexico.

The researchers targeted Chicxulub crater’s peak ring and overlying rock sequences.

“Peak rings, as seen on the Moon, form when rocks rebound into a peak inside the crater. The peak then collapses, leaving a center ring of rock within the larger crater,” they explained.

IODP-ICDP Expedition 364 drilled into the subsurface Chicxulub peak ring at borehole M0077A (red dot), which was about 30 km northwest of Progreso and the north shore of the Yucatán Peninsula. The blue circle represents the approximate diameter of the 180-200-km subsurface impact structure. The gravity signature of the structure and locations of other drilling sites are shown in the inset. The only two sites with continuous core are the ICDP Yaxcopoil-1 (Yax-1) and IODP-ICDP M0077A boreholes. Other boreholes are Yucatán-1 (Y1), Yucatán-2 (Y2), Yucatán-6 (Y6), Chicxulub-1 (C1), Sacapuc-1 (S1), and Ticul-1 (T1). Image credit: Kring et al, doi: 10.1130/GSATG352A.1.

IODP-ICDP Expedition 364 drilled into the subsurface Chicxulub peak ring at borehole M0077A (red dot), which was about 30 km northwest of Progreso and the north shore of the Yucatán Peninsula. The blue circle represents the approximate diameter of the 180-200-km subsurface impact structure. The gravity signature of the structure and locations of other drilling sites are shown in the inset. The only two sites with continuous core are the ICDP Yaxcopoil-1 (Yax-1) and IODP-ICDP M0077A boreholes. Other boreholes are Yucatán-1 (Y1), Yucatán-2 (Y2), Yucatán-6 (Y6), Chicxulub-1 (C1), Sacapuc-1 (S1), and Ticul-1 (T1). Image credit: Kring et al, doi: 10.1130/GSATG352A.1.

The IODP-ICDP borehole data indicate that the peak-ring morphology of the Chicxulub crater was produced by the dynamic collapse of an uplifted central peak.

Drilling also confirmed that the peak ring at Chicxulub consists of granite, brought up from mid-crustal depths.

“The Chicxulub impact generated an environmental calamity that extinguished life. It also induced a vast sub-surface hydrothermal system that altered a portion of the Maya Block and serves as a proxy for much larger and more frequently generated hydrothermal systems during the Hadean, when bombardment rates were high,” the scientists said.

They estimated the amount of sulfur and carbon dioxide shot into the atmosphere, including a second phase of gas release when ejecta was re-vaporized.

“Release of gas from the Chicxulub impact is connected to cooling of over 20 degrees Celsius, with sub-freezing temperatures for three years,” the researchers said.

They also found that soon after the impact the crater became an oasis for the recovery of life and allowed expansion into momentarily vacant niches that, when filled, defined the modern world.

“We followed the recovery of life at ground zero, focusing on an 80-cm transitional layer and the limestone just above,” they said.

“These units record the devastation of the impact, trace fossils from surviving species, and fossils within the limestone revealing that within 30,000 years of impact, life inside the crater was back in full swing.”

The findings were published in the October 2017 issue of the journal GSA Today and presented yesterday at the GSA Annual Meeting in Seattle, Washington.

Researchers Piece Together Bread Wheat Genome

An international team of scientists from the Johns Hopkins University, Pacific Biosciences, and Earlham Institute has produced the first near-complete genomic sequence for the common bread wheat (Triticum aestivum). The research appears in the journal GigaScience.

A field of bread wheat (Triticum aestivum) in Ukraine. Image credit: Oleksii Alieksieiev.

A field of bread wheat (Triticum aestivum) in Ukraine. Image credit: Oleksii Alieksieiev.

Bread wheat has one of the most complex genomes known to science, with 6 copies of 7 chromosomes, enormous numbers of near-identical sequences scattered throughout, and an overall size of almost 16 billion base pairs of DNA.

By comparison, the human genome is about 5 times smaller, with about 3 billion base pairs and two copies of 23 chromosomes.

“After many years of trying, we’ve finally been able to produce a high-quality assembly of this very challenging genome,” said Professor Steven Salzberg, from the Johns Hopkins University Schools of Engineering and Medicine.

Previously published versions of the bread wheat genome have contained large gaps in its highly repetitive DNA sequence.

“The repetitive nature of this genome makes it difficult to fully sequence. It’s like trying to put together a jigsaw puzzle of a landscape scene with a huge blue sky. There are lots of very similar, small pieces to assemble,” Professor Salzberg said.

The newly assembled bread wheat genome took a year for the team to assemble 1.5 trillion bases of raw data into a final assembly of 15.34 billion base pairs.

To do it, the authors used two types of genome sequencing technology: high throughput and nanopore sequencing.

“As its name implies, high throughput sequencing generates massive amounts of DNA base pairs very quickly and cheaply, although the fragments are very short — just 150 base pairs long for this project,” the researchers explained.

“To help assemble the repetitive areas, we used nanopore sequencing, which forces DNA through tiny pores with an electric current running through them. The technology enables us to read up to 20,000 base pairs at a time by measuring changes in the flow of the current as a strand of DNA passes through the pore.”

The newly-assembled bread wheat genome sequence and the recently-published sequence of the bread wheat’s ‘ancestor,’ the Tausch’s goatgrass (Aegilops tauschii), may help biologists not only better understand the evolutionary history of wheat, but also advance the quest for hardier, more pest- and drought-resistant wheat types to help feed the world’s growing population.

Coffee Consumption ‘More Likely to Benefit Health Than To Harm It’

Drinking three to four cups of coffee a day is associated with a lower risk of mortality and getting heart disease compared with drinking no coffee, according to an umbrella review of over 200 previous studies, published in the journal BMJ.

According to the scientists, coffee consumption is generally safe, but doctors should not recommend drinking coffee to prevent disease -- and people should not start drinking coffee for health reasons. Image credit: Myriams Fotos.

According to the scientists, coffee consumption is generally safe, but doctors should not recommend drinking coffee to prevent disease — and people should not start drinking coffee for health reasons. Image credit: Myriams Fotos.

Coffee is one of the most commonly consumed beverages worldwide. As such, even small individual health effects could be important on a population scale.

But existing evidence is of lower quality from observational research and randomized controlled trials are needed to strengthen the evidence of benefits.

To better understand the effects of coffee consumption on health, University of Southampton researcher Dr. Robin Poole and co-authors carried out a review of 201 studies that had aggregated data from observational research and 17 studies that had aggregated data from clinical trials across all countries and all settings.

Drinking coffee was consistently associated with a lower risk of mortality from all causes and from heart disease, with the largest reduction in relative risk of mortality at three cups a day, compared with non-coffee drinkers.

Increasing consumption to above three cups a day was not associated with harm, but the beneficial effect was less pronounced.

Coffee was also associated with a lower risk of several cancers, including prostate, endometrial, skin and liver cancer, as well as type 2 diabetes, gallstones and gout.

The greatest benefit was seen for liver conditions, such as cirrhosis of the liver.

Finally, there seemed to be beneficial associations between coffee consumption and Parkinson’s disease, depression and Alzheimer’s disease.

There was less evidence for the effects of drinking decaffeinated coffee but it had similar benefits for a number of outcomes.

“However, drinking coffee in pregnancy may be associated with harms, and may be linked to a very small increased risk of fracture in women,” the authors said.

“Excluding pregnancy and women at risk of fracture, coffee drinking appears safe within usual patterns of consumption,” they concluded.

“We call for robust randomized controlled trials to understand whether the key observed associations are causal.”

Earth Can Absorb High-Energy Neutrinos, Physicists Find

Neutrinos are subatomic particles that are famous for passing through anything and everything. Now, physicists have demonstrated that our planet stops high-energy neutrinos — they do not go through everything. The experiment was achieved with the IceCube Observatory, an array of 5,160 basketball-sized sensors frozen deep within a km3 of very clear ice near the South Pole.

This image shows a visual representation of one of the highest-energy neutrino detections superimposed on a view of the IceCube Observatory at the South Pole. Image credit: IceCube Collaboration.

This image shows a visual representation of one of the highest-energy neutrino detections superimposed on a view of the IceCube Observatory at the South Pole. Image credit: IceCube Collaboration.

Neutrinos are among the most abundant particles in the cosmos. With almost no mass and no charge, they rarely interact with matter. Tens of trillions of neutrinos course through our bodies every second.

Theory predicts that at high energies — higher than can be generated by any earthbound particle accelerator — neutrinos can be expected to interact with matter and be absorbed in the Earth instead of continuing to transit the cosmos.

The first detections of extremely-high-energy neutrinos were made by the IceCube Observatory in 2013, but the mystery remained.

“We knew that lower-energy neutrinos pass through just about anything, but although we had expected higher-energy neutrinos to be different, no previous experiments had been able to demonstrate convincingly that higher-energy neutrinos could be stopped by anything,” said Penn State Professor Doug Cowen.

“We always say that no particle but the neutrino can go through the Earth,” added IceCube principal investigator Professor Francis Halzen, from the University of Wisconsin-Madison.

“However, the neutrino does have a tiny probability to interact, and this probability increases with energy. That probability is what scientists call the neutrino cross section.”

The new IceCube measurement determined the cross section for neutrino energies between 6.3 TeV and 980 TeV, energy levels more than an order of magnitude higher than previous measurements. The most energetic neutrinos studied so far from earthbound accelerators are at the 0.4 TeV energy level.

“IceCube’s sensors do not directly observe neutrinos, but instead measure flashes of blue light, known as Cherenkov radiation, emitted after a series of interactions involving fast-moving charged particles that are created when neutrinos interact with the ice,” the physicists said.

“By measuring the light patterns from these interactions in or near the detector array, IceCube can estimate the neutrinos’ energies and directions of travel.”

Analyzing a year of IceCube data gathered between May 2010 and May 2011, they put 10,800 neutrino interactions under the microscope.

“We looked mostly at neutrinos created when high-energy cosmic rays crash into the nuclei of nitrogen or oxygen in the Earth’s atmosphere. Those collisions produce a cascade of subatomic particles that can generate neutrinos,” they said.

“The sample also included a smaller number of neutrinos probably created in yet-to-be identified cosmic accelerators such as black holes.”

“We found that fewer of the most energetic neutrinos were making it to the detector from the northern hemisphere, where the particles would have to transit the entire Earth, including the dense core of our planet, before reaching the IceCube sensors. From less obstructed, near horizontal trajectories, more neutrinos were detected.”

The IceCube measurements conform to the Standard Model of particle physics.

“In the absence of new physics, the Standard Model allows us to calculate the neutrino-proton cross section at the energies probed by IceCube,” Professor Halzen said.

“What we measure is consistent — up to now — with what is expected. We were of course hoping for some new physics to appear, but we unfortunately find that the Standard Model, as usual, withstands the test.”

“However, the advantage of IceCube is its ability to measure the highest energy neutrinos, which are produced in cosmic accelerators — supermassive black holes, the violent hearts of star-forming galaxies, and galaxy clusters — that no accelerator on Earth can match,” he added.

“If, for example, IceCube data harbor evidence of neutrinos with cross sections greater than what scientists have calculated using the Standard Model, it could invoke new physics such as compact, hidden spatial dimensions.”