Europe took center-stage in global spread of the coronavirus, says new research

A collaboration between genome researchers at the University of Huddersfield and Portugal’s University of Minho has led to one of the largest analyses of its kind focusing on thousands of virus genomes sampled from all around the world.

The University of Huddersfield’s Archaeogenetics Research Group has mapped out the dispersal of the SARS-CoV-2 coronavirus, responsible for the current worldwide COVID-19 pandemic, putting Europe centre-stage as the main source of the spread.

The group’s findings, recently published in a special issue of the peer-reviewed journal Microorganisms, confirm that the virus originated in China and most likely jumped into humans from horseshoe bats. But that it is Europe, not China, which has been the main source for spreading the disease around the world.

The research also suggests that travel restrictions across Britain and Europe seem to have been too little and too late and that the actual spread of the virus to America and other parts of the world was largely via Europe, and not directly from China.

The study focused on 27,000 virus genomes, sampled from all around the world. The researchers usually work on tracking ancient human migrations using mitochondrial DNA, and they capitalised on the fact that the virus genome is similar in crucial respects.

Still, the mammoth size of the database, even back in May when the study began, makes this one of the biggest analyses of its kind ever undertaken.

The intensive data analyses were carried out by clinical geneticist Dr Teresa Rito and evolutionary geneticist Dr Pedro Soares. Both are based at the University of Minho, in Portugal and have worked closely with the University of Huddersfield’s Professor Martin Richards and Dr Maria Pala, as part of the Archaeogenetics Research Group, on many occasions. The pair called upon the knowledge and expertise of their colleagues in the UK to help make sense of the data and publish their conclusions in double-quick time.

Professor Richards explained how there is a huge ongoing worldwide effort to understand the spread of the coronavirus and that researchers are trying to make their work available to the public as fast as possible.

As the world continues to face a rapidly spreading pathogen, Dr Pala believes a greater understanding of the virus will better inform and improve upon policies designed to control the spread.

“With thousands of lives still at risk,” added Dr Pala, “the need for scientific research is now more crucial than ever.”

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Materials provided by University of Huddersfield. Note: Content may be edited for style and length.

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NaNoWriMo – Day 2

On Day 2 of NaNoWriMo, I wrote 1743 more words, so I’m at 3439 words for my novel so far. Today I’ll pass 5K words.

While the challenge is technically to write 50K words in 30 days, I’m framing it as a daily commitment to write at least 1667 words per day. So I’ll surely end up with more than 50K words by the end. My approach is less flexible since I won’t be taking any days off, nor will I reduce the daily quota based on my ongoing word count. It’s easier for me this way since I’ll never let myself fall behind, so I’ll avoid the trap of having to write thousands of extra words to catch up later. Today is Day 3, and some people are already feeling behind because they didn’t write much on the first two days. I’d rather always feel like I’m ahead for the rest of the month. I’m ahead in my word count now, and I’m going to pad my lead each day going forward. I will never be behind, only ahead.

As I’ve noted many times before, you win a 30-day challenge before you start Day 1. It’s all in the early game. I’m well aware of the tricks and traps my mind will succumb to if I don’t frame and approach the challenge correctly, so I remove the riskiest excuses in advance. Sometimes that means being extra strict, but there’s a hidden ease and lightness in that strictness that many people overlook.

I also feel compassion for my future self, so I won’t to burden him with having to do a 5K- or 10K-word catch-up day this month. If he wants to blast out more words for fun because he wants to, he has that option, but I won’t force that obligation onto him. I’m just going to stick with a steady pacing one day at a time.

I began Day 2 by re-reading what I wrote on Day 1, fixing a couple of typos and making a few more editing notes but otherwise not doing any editing. I just want to focus on writing to get the ideas down. Some Nano participants have cautioned that it’s risky to re-read previous work during the challenge since they too easily get sucked into editing, which doesn’t advance their word count. I don’t find that to be an issue so far though. Making some editing notes is enough for me. I might toss out entire scenes later, so I don’t see the point in editing them prematurely. I see this as being similar to optimizing code that was written for a prototype, which is usually pointless since that code will likely be refactored or replaced anyway. Since I’m just prototyping my novel, sloppy code (or writing) is fine for now. Little or nothing of what I write for this draft is likely to make it into the final version.

I take to heart the advice that the purpose of the first draft is to write the story for myself. That mindset is helpful since it encourages me to just explore the ideas and possibilities and not fuss over how bad it is.

This time I wrote two shorter scenes of roughly equal length, so I have three scenes done now. Instead of writing two more scenes in order though, I skipped ahead and wrote the first two scenes of Act II. So I still have more to fill in for Act I, but I like that this helps me see one of the upcoming signposts that I want to reach. I think I have a better sense of where to take Act I now that I see how Act II begins.

I recently learned about James Scott Bell’s 14-signpost plot structure, and I like it so far. It fits my novel idea pretty well, so I’m loosely using it for my scaffolding. I think it’s more useful and insightful than the common 7-point plot structure or the 12-point hero’s journey or any of the other structures I’ve seen so far.

Within this signpost model, I wrote signpost scene #1 on Day 1 (The Disturbance), and on Day 2 I wrote signpost scene #5 (Doorway of No Return #1), along with another scene right after after signpost scene #5.

However, after that writing session, I did more reading about this structure, and I realized that it would probably be wise to insert signpost scene #6 (A Kick in the Shins) immediately after signpost scene #5.

In The Matrix movie, think of signpost scene #5 as the scene where Neo decides to take the red pill. That’s his first doorway of no return. What happens immediately after that? He swallows the pill, and now he’s on his way out of the Matrix. He touches a mirror, which sticks to him and then spreads over his skin, making him freak out. The crew makes it clear that his life is in danger while they race against time to trace his signal. Then Neo’s real human body wakes up – hairless, naked, and covered in slime. Eventually he gets dumped down a chute and picked up by Morpheus’ ship. But now he’s really weak and has to build up muscles he’s never used. I think that’s a good example of signpost scene #6 (A Kick in the Shins) following immediately after signpost scene #5 (Doorway of No Return #1).

The purpose of giving the protagonist a kick in the shins right after they commit to a new course of action is to show that the stakes are indeed high – often life or death. Neo doesn’t just take the red pill and find himself dancing with Smurfs. He’s blasted with some hefty seriousness, and the risks become more real and present. Notice what this does for the pacing and tension of the story. Imagine how Act II would flow if there was no kick in the shins. The tension and momentum would drop, and the pacing would feel slower.

I find it empowering to study story structure as I go along. This way I can connect my actual writing to the structural elements I’m learning, so the study is immediately practical. Bell’s signpost structure helps me think about the next signpost coming up that I can aim for, so there’s a purposeful progression to what I’m writing.

While I don’t have to use a known structure as a guide, it sure is helpful when just starting out. It’s also fun and rewarding to spot these structural elements in books and movies, like The Matrix. Once you see those patterns, you cannot unsee them.

I’d like to spend some time watching more classic movies this month to ponder their structure. I really enjoyed the deep analysis that was done at Robert McKee’s Story seminar last year, where we took six hours to go through Casablanca scene by scene. That gave me a whole new appreciation of the movie.

Overall the writing process on Day 2 was slower going than Day 1, taking about 90 minutes. I had to pause and think more about the character interactions and action flow. I really notice how inefficient my mental circuitry is at writing fiction. When I write nonfiction articles, ideas flow in and words flow out with nary a hint of friction or resistance. My subconscious constructs sentences and paragraphs for me. I watch as my fingers type. Editing is super easy too.

But with fiction it’s a whole different story (pun intended). It feels like I’m using brain circuitry that’s clogged with sludge. Ideas flow in, but they get bogged down in mental marshland, occasionally spitting out gobs of muddy language. I have to consciously push my thoughts through the tubes, just to get some ill-formed words and phrases splattering onto the screen. My mind pops and stutters in confusion. It takes real mental effort just to squeeze out one sentence at a time. And it’s way more taxing and draining.

Writing a nonfiction blog post about my fiction writing is so much easier and more effortless than writing the fiction itself.

These experiences are very different emotionally too. Blogging usually feels delightful – so light, playful, meaningful, flowing, and graceful as my fingers dance and skip around the keys like happy kids playing hopscotch.

Writing fiction feels darker for me. There’s tension, tightness, and awkwardness in the experience. It’s like I’m back in school doing a mandatory speech contest – a dreadful experience that I hated. But then when the day’s writing is done, there’s a feeling of relief, and I can breathe easier again.

It would be wonderful to reach the point where fiction content flows through my mind with the same ease as nonfiction. Maybe in a million words or so, I’ll be at that point. In the meantime I’m okay with the friction phase, which slows me down but doesn’t stop me. Lots of learning experiences are like this in the beginning.

Here are two things that helped:

  • Before I started writing, I did a quick journaling Q&A with the main character to ask her what she wanted me to write today and how she wanted me to express her character. She gave me some suggestions on ways to express more personality for her. This was harder to write at first, but it made for more interesting (less bland) dialogue. I’m gradually feeling more connected with this character.
  • Listening to brain.fm focus tracks while writing is wonderful for reducing the mental and emotional tension. It helps me relax into the creative writing experience.

Onward to Day 3…

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Covid-19: Liverpool to pilot city-wide coronavirus testing

It will use rapid results tests that could be offered to “millions” by Christmas, the PM says.

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Covid: Deaths 10% higher than normal as virus deaths rise

There were nearly 12,300 deaths in latest week – 1,100 linked to Covid.

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New simulation finds max cost for cost-effective health treatments

As health care costs balloon in the U.S., experts say it may be important to analyze whether those costs translate into better population health. A new study led by a Penn State researcher analyzed existing data to find a dividing line — or “threshold — for what makes a treatment cost-effective or not.

David Vanness, professor of health policy and administration, led a team of researchers that created a simulation to consider health care treatment costs, insurance premiums, quality of life, and life expectancy to explore whether a treatment delivers enough value for its costs to be considered beneficial for population health.

According to Vanness, the term “treatment cost” in this research incorporates all the costs and savings related to a treatment. For example, the cost of a treatment to lower blood cholesterol would include how much it costs but also take into account potential savings for preventing a heart attack and its subsequent treatment.

“We know that we are spending more and more on health care in the U.S. and that we’re getting less and less for it,” Vanness said. “We do a good job of developing new treatments in this country, but we don’t do a good job of covering everybody or making sure that people have access to basic health care. We’re spending a lot on our medical treatments, but many of those treatments just don’t have a lot of value.”

Vanness added that in order to improve a population’s health without spending too much, it’s important to be able to tell whether the prices drug and device manufacturers are charging are justified by what they deliver in health improvements.

The researchers found that in their simulation, for every $10,000,000 increase in health care expenditures, 1860 people became uninsured. This led to five deaths, 81 quality-adjusted life-years lost due to death, and 15 quality-adjusted life-years lost due to illness. In health care economics, one quality-adjusted life-year (QALY) is equal to one year of perfect health.

Vanness said these results — recently published in the Annals of Internal Medicine — suggests a cost effectiveness threshold of $104,000 per QALY.

“If a treatment is beneficial but it costs more than about $100,000 to gain one quality-adjusted life-year using that treatment, then it may not be a good deal,” Vanness said. “Because our simulation was using data estimates, we wanted to come up with a range of plausible values. So anything over a range of $100,000 to $150,000 per QALY gained is likely to actually make our population’s health fall.”

To create the simulation, Vanness said he and the other researchers used a variety of data, starting with estimates about how likely people are to drop their insurance when their premiums go up.

“We also used evidence from the public health literature on what happens to people’s health and mortality when they gain or lose health insurance,” Vanness said.

The simulation then compiled that data and estimated how much the health of a population goes down when costs increase. According to Vanness, that relationship determines the cost-effectiveness threshold — how much a treatment can cost relative to the health benefits it gives before it causes more harm than good.

The researchers said the findings could be especially important to organizations like the Institute for Clinical and Economic Review, which provides analysis to several private and public insurers to help negotiate prices with manufacturers. These organizations could use the findings as empirical evidence for what makes a treatment a good value in the U.S.

“Moving forward, I think some changes could be made to national policy to make cost effectiveness analysis more commonly used,” Vanness said. “Our goal is to get that information out there with the hope that somebody is going to use it to help guide coverage or maybe get manufacturers to reduce their prices on some of these drugs.”

James Lomas, University of York, and Hannah Ahn, a Penn State graduate students, also participated in this work.

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Materials provided by Penn State. Original written by Katie Bohn. Note: Content may be edited for style and length.

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‘Transparent solar cells’ can take us towards a new era of personalized energy

Today, the imminent climate change crisis demands a shift from conventionally used fossil fuels to efficient sources of green energy. This has led to researchers looking into the concept of “personalized energy,” which would make on-site energy generation possible. For example, solar cells could possibly be integrated into windows, vehicles, cellphone screens, and other everyday products. But for this, it is important for the solar panels to be handy and transparent. To this end, scientists have recently developed “transparent photovoltaic” (TPV) devices — transparent versions of the traditional solar cell. Unlike the conventionally dark, opaque solar cells (which absorb visible light), TPVs make use of the “invisible” light that falls in the ultraviolet (UV) range.

Conventional solar cells can be either “wet type” (solution based) or “dry type” (made up of metal-oxide semiconductors). Of these, dry-type solar cells have a slight edge over the wet-type ones: they are more reliable, eco-friendly, and cost-effective. Moreover, metal-oxides are well-suited to make use of the UV light. Despite all this, however, the potential of metal-oxide TPVs has not been fully explored until now.

To this end, researchers from Incheon National University, Republic of Korea, came up with an innovative design for a metal-oxide-based TPV device. They inserted an ultra-thin layer of silicon (Si) between two transparent metal-oxide semiconductors with the goal of developing an efficient TPV device. These findings were published in a study in Nano Energy, which was made available online on August 10, 2020 (ahead of the scheduled final publication in the December 2020 issue). Prof Joondong Kim, who led the study, explains, “Our aim was to devise a high-power-producing transparent solar cell, by embedding an ultra-thin film of amorphous Si between zinc oxide and nickel oxide.”

This novel design consisting of the Si film had three major advantages. First, it allowed for the utilization of longer-wavelength light (as opposed to bare TPVs). Second, it resulted in efficient photon collection. Third, it allowed for the faster transport of charged particles to the electrodes. Moreover, the design can potentially generate electricity even under low-light situations (for instance, on cloudy or rainy days). The scientists further confirmed the power-generating ability of the device by using it to operate the DC motor of a fan.

Based on these findings, the research team is optimistic that the real-life applicability of this new TPV design will soon be possible. As for potential applications, there are plenty, as Prof Kim explains, “We hope to extend the use of our TPV design to all kinds of material, right from glass buildings to mobile devices like electric cars, smartphones, and sensors.” Not just this, the team is excited to take their design to the next level, by using innovative materials such as 2D semiconductors, nanocrystals of metal-oxides, and sulfide semiconductors. As Prof Kim concludes, “Our research is essential for a sustainable green future — especially to connect the clean energy system with no or minimal carbon footprint.”

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Materials provided by Incheon National University. Note: Content may be edited for style and length.

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Self-watering soil could transform farming

 A new type of soil created by engineers at The University of Texas at Austin can pull water from the air and distribute it to plants, potentially expanding the map of farmable land around the globe to previously inhospitable places and reducing water use in agriculture at a time of growing droughts.

As published in ACS Materials Letters, the team’s atmospheric water irrigation system uses super-moisture-absorbent gels to capture water from the air. When the soil is heated to a certain temperature, the gels release the water, making it available to plants. When the soil distributes water, some of it goes back into the air, increasing humidity and making it easier to continue the harvesting cycle.

“Enabling free-standing agriculture in areas where it’s hard to build up irrigation and power systems is crucial to liberating crop farming from the complex water supply chain as resources become increasingly scarce,” said Guihua Yu, associate professor of materials science in the Walker Department of Mechanical Engineering.

Each gram of soil can extract approximately 3-4 grams of water. Depending on the crops, approximately 0.1 to 1 kilogram of the soil can provide enough water to irrigate about a square meter of farmland.

The gels in the soil pull water out of the air during cooler, more humid periods at night. Solar heat during the day activates the water-containing gels to release their contents into soil.

The team ran experiments on the roof of the Cockrell School’s Engineering Teaching Center building at UT Austin to test the soil. They found that the hydrogel soil was able to retain water better than sandy soils found in dry areas, and it needed far less water to grow plants.

During a four-week experiment, the team found that its soil retained approximately 40% of the water quantity it started with. In contrast, the sandy soil had only 20% of its water left after just one week.

In another experiment, the team planted radishes in both types of soil. The radishes in the hydrogel soil all survived a 14-day period without any irrigation beyond an initial round to make sure the plants took hold. Radishes in the sandy soil were irrigated several times during the first four days of the experiment. None of the radishes in the sandy soil survived more than two days after the initial irrigation period.

“Most soil is good enough to support the growth of plants,” said Fei Zhao, a postdoctoral researcher in Yu’s research group who led the study with Xingyi Zhou and Panpan Zhang. “It’s the water that is the main limitation, so that is why we wanted to develop a soil that can harvest water from the ambient air.”

The water-harvesting soil is the first big application of technology that Yu’s group has been working on for more than two years. Last year, the team developed the capability to use gel-polymer hybrid materials that work like “super sponges,” extracting large amounts of water from the ambient air, cleaning it and quickly releasing it using solar energy.

The researchers envision several other applications of the technology. It could potentially be used for cooling solar panels and data centers. It could expand access to drinking water, either through individual systems for households or larger systems for big groups such as workers or soldiers.

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Materials provided by University of Texas at Austin. Note: Content may be edited for style and length.

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Coronavirus lockdown: PM warns UK faces ‘medical disaster’ without action

Boris Johnsons says lockdown rules will expire on 2 December – with MPs to vote on what happens next.

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T-cell response ‘lasts six months after Covid infection’

But it is still not clear how much this protects people against being re-infected, experts say.

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Covid: Target ‘hit’ for 500,000 tests a day in the UK

Network of mega-labs and use of over 100 small labs increases capacity for testing.

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