Newsworthy Science

Duplicating a single gene in rice boosts output by 40%

Improvements in agricultural productivity could lessen the impact of agriculture on the environment and perhaps supply more food from less land. Working in rice, Wei et al. identified a transcription factor that, when overexpressed, has a variety of useful effects. The gene’s expression is induced by both light and low-nitrogen status, and it regulates photosynthetic capacity, nitrogen utilization, and flowering time. In field trials, plants overexpressing this gene delivered greater yield, shortened growth duration, and improved nitrogen use efficiency.​
Overexpression of OsDREB1C not only boosts grain yields but also confers higher NUE and early flowering. Our work demonstrates that by genetically modulating the expression of a single transcriptional regulator gene, substantial yield increases can be achieved while the growth duration of the crop is shortened. The existing natural allelic variation in OsDREB1C, the highly conserved function of the transcription factor in seed plants, and the ease with which its expression can be altered by genetic engineering suggest that this gene could be the target of future crop improvement strategies toward more efficient and more sustainable food production.​

Paper Writeup Perspective

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The proportion of total habitable land that is wild versus farmed has decreased over time (top left). Additionally, the amount of people fed per hectare has increased, owing to technological improvements (bottom left). However, this is not enough to feed the human population, so further yield gains are needed. Photosynthetic rate is highly variable in different plant species (right), indicating that improvements to photosynthesis, and thus yield, are possible.
 
Well, the DeepMind, AlphaFold lot are claiming to have solved one of the big unsolved problems of biosciences:

https://www.theguardian.com/technol...e-of-200m-proteins-in-scientific-leap-forward

Artificial intelligence has deciphered the structure of virtually every protein known to science, paving the way for the development of new medicines or technologies to tackle global challenges such as famine or pollution.

Proteins are the building blocks of life. Formed of chains of amino acids, folded up into complex shapes, their 3D structure largely determines their function. Once you know how a protein folds up, you can start to understand how it works, and how to change its behaviour. Although DNA provides the instructions for making the chain of amino acids, predicting how they interact to form a 3D shape was more tricky and, until recently, scientists had only deciphered a fraction of the 200m or so proteins known to science.


In November 2020, the AI group DeepMind announced it had developed a program called AlphaFold that could rapidly predict this information using an algorithm. Since then, it has been crunching through the genetic codes of every organism that has had its genome sequenced, and predicting the structures of the hundreds of millions of proteins they collectively contain.

This is one of those claims that is huge if true. As XKCD put it:

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Given that I spent the better part of three years of my PhD figuring out the structures of just a few proteins in a complex, and that was only just over a decade ago, this would certainly speed things up massively. There has been protein structure prediction software before of course - they existed even back then - but they needed a lot more than the simple protein sequence to work with and the results were - well, marginally better than random guesswork, but that was about the best you could say.

Last year, DeepMind published the protein structures for 20 species – including nearly all 20,000 proteins expressed by humans – on an open database. Now it has finished the job, and released predicted structures for more than 200m proteins.

I was curious enough to look up their structures for the proteins I worked on back in my PhD (yep, they're all in there), and I'm impressed with DeepMind's predictions. The secondary structures are pretty much all spot on, aside from a couple of helices it's tried to see in a lengthy unstructured flexible linker (and which it's labelled as low confidence). The tertiary structure is certainly very close to what I deduced. The structured domains are all there and quite recognizable. Perhaps a little squashed looking in a couple of places compared to the images I figured out experimentally for my thesis, but these proteins have a fair amount of "squashiness" to them anyway.

I'll be curious to see if we get to the point where I can just grab a protein structure out of this database and take it as reasonably likely to be accurate. It would certainly make things so much faster.
 
Well, the DeepMind, AlphaFold lot are claiming to have solved one of the big unsolved problems of biosciences:

https://www.theguardian.com/technol...e-of-200m-proteins-in-scientific-leap-forward



This is one of those claims that is huge if true. As XKCD put it:

proteins.png


Given that I spent the better part of three years of my PhD figuring out the structures of just a few proteins in a complex, and that was only just over a decade ago, this would certainly speed things up massively. There has been protein structure prediction software before of course - they existed even back then - but they needed a lot more than the simple protein sequence to work with and the results were - well, marginally better than random guesswork, but that was about the best you could say.



I was curious enough to look up their structures for the proteins I worked on back in my PhD (yep, they're all in there), and I'm impressed with DeepMind's predictions. The secondary structures are pretty much all spot on, aside from a couple of helices it's tried to see in a lengthy unstructured flexible linker (and which it's labelled as low confidence). The tertiary structure is certainly very close to what I deduced. The structured domains are all there and quite recognizable. Perhaps a little squashed looking in a couple of places compared to the images I figured out experimentally for my thesis, but these proteins have a fair amount of "squashiness" to them anyway.

I'll be curious to see if we get to the point where I can just grab a protein structure out of this database and take it as reasonably likely to be accurate. It would certainly make things so much faster.
The thing is about this, is they have predicted a load of structures, but the hard ones have no actually assessed structure so how do they know if they are right? The way AlphaFold works is by using similar pre-existing structures. For those hard ones that we cannot crystalise anything like it then what have they to go on, how can they make a prediction, and how can that prediction be tested?

I am sure this is going to change the world in the coming years, but I am not sure this is being reported very accurately.
 
The thing is about this, is they have predicted a load of structures, but the hard ones have no actually assessed structure so how do they know if they are right? The way AlphaFold works is by using similar pre-existing structures. For those hard ones that we cannot crystalise anything like it then what have they to go on, how can they make a prediction, and how can that prediction be tested?

There's a lot of biophysical techniques which would be up to corroborating an existing model, even if they aren't able to generate a structure from scratch. From AlphaFold's predicted models you could make a lot of predictions about e.g. hydrophobic patches, charged surfaces, solvent exposure, which you could then test in the solution state.

From my own area, there's quite a few proteins with no crystal data, but partial solution NMR data (e.g. nuclear Overhauser effect restraints). Not enough of them to work out a protein structure in themselves, but it's a much more straightforward task to check if these restraints are consistent with any presented model for the protein.

I'm going to be cautious on this one as well - it's a huge claim, so it needs huge evidence. But I was pleasantly surprised when I checked their database for my own structures. I was expecting a vague resemblance, probably a step up from secondary structure prediction programs. They're a lot better than I expected.
 
Ironclad snails use symbiotic bacteria to extract energy from hydrothermal vents

“It looks like an armoured knight crawling around on the deep-sea floor,” says Julia Sigwart, a biologist at Frankfurt’s Senckenberg Research Institute and one of the only people to have seen a living scaly-foot snail (Chrysomallon squamiferum), also known as a sea pangolin.​
The snails’ habitat is extreme. They live several miles below the ocean surface on searing hydrothermal vents, which are bathed in toxic chemicals and can reach temperatures of more than 300C (572F).​
The snails’ entire bodies and lifestyles revolve around bacteria growing inside a special pouch in their throat, which convert chemicals pouring out of the vents into energy and thereby provide all the snails’ food.​
To keep their microbes well fed, scaly-foot snails evolved enormous gills to absorb oxygen and chemicals from seawater, then deliver it by way of their bloodstream and a hugely capacious heart. A human heart of equivalent proportions would be the size of our heads.​
In 2019, scientists worked out that the scales on the snails’ foot are not to protect against predatory attack but to avert a toxic threat that comes from within. The bacteria stashed in a scaly-foot snail’s throat release sulphur as a waste product, which is deadly to snails (it’s a common active ingredient in slug and snail-killing pellets).​
The internal structure of their scales acts as tiny exhaust pipes, drawing the dangerous sulphur away from the snails’ soft tissues and depositing it as a harmless iron-based compound on the outside.​
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Ironclad snails use symbiotic bacteria to extract energy from hydrothermal vents

“It looks like an armoured knight crawling around on the deep-sea floor,” says Julia Sigwart, a biologist at Frankfurt’s Senckenberg Research Institute and one of the only people to have seen a living scaly-foot snail (Chrysomallon squamiferum), also known as a sea pangolin.​
The snails’ habitat is extreme. They live several miles below the ocean surface on searing hydrothermal vents, which are bathed in toxic chemicals and can reach temperatures of more than 300C (572F).​
The snails’ entire bodies and lifestyles revolve around bacteria growing inside a special pouch in their throat, which convert chemicals pouring out of the vents into energy and thereby provide all the snails’ food.​
To keep their microbes well fed, scaly-foot snails evolved enormous gills to absorb oxygen and chemicals from seawater, then deliver it by way of their bloodstream and a hugely capacious heart. A human heart of equivalent proportions would be the size of our heads.​
In 2019, scientists worked out that the scales on the snails’ foot are not to protect against predatory attack but to avert a toxic threat that comes from within. The bacteria stashed in a scaly-foot snail’s throat release sulphur as a waste product, which is deadly to snails (it’s a common active ingredient in slug and snail-killing pellets).​
The internal structure of their scales acts as tiny exhaust pipes, drawing the dangerous sulphur away from the snails’ soft tissues and depositing it as a harmless iron-based compound on the outside.​
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'Fake It Till You Make It' Isn't Just A Cliché. It's Backed By Science.​

The concept is more formally called "behavioral activation." Here's how it can help your mental health.

The phrase “fake it till you make it” can feel like a cliché, but there’s some value to this idea in the mental health field.
The expression is often evoked in describing the concept of behavioral activation ― a useful tool in managing conditions like depression and anxiety. But what exactly is this approach, and how does it compare to the idea of “faking” confidence, competence or positive emotions in order to achieve results?
Below, mental health professionals break down the meaning and effects of behavioral activation, as well as the best ways to apply this technique in your everyday life.

What is behavioral activation?

“Behavioral activation is a concept and intervention frequently used in cognitive behavioral therapy that utilizes behaviors to influence emotions, thoughts and mood,” said Rachel Thomasian, a licensed therapist and owner of Playa Vista Counseling in Los Angeles. “In other words, a therapist will often prescribe behaviors for their client to take part in, with the expectation that it will modify or ease some painful emotion they might be experiencing, such as anxiety or depression.”

AN ESSENTIAL DAILY GUIDE TO ACHIEVING THE GOOD LIFE​

A common symptom of depression is the inability to engage in behaviors that used to bring a person joy ― even though those behaviors would likely help alleviate their depression. Examples include socializing, exercising, cooking nice meals, self-pampering with showers and skin care routines, trying new activities and more.
“Instead, people who are feeling sad or lonely may seek out situations or fall into patterns that confirm their feelings of isolation and sadness,” said Meg Gitlin, a New York-based psychotherapist who runs the Instagram account @citytherapist. “This can be seen as somewhat of a self-fulfilling prophecy or a downward spiral. Behavioral activation requires you to consider the alternate ― that is, that by planning out activities and rewards that once brought you pleasure, it’s likely that you will experience those same good feelings once completed.”

How does it work?
“Our mental health and emotional state is so tied to the behaviors we engage in,” Thomasian said. “Deciding to stay in bed and going on a morning walk release very different chemicals in our brain, create starkly varying thoughts in our mind that then reinforce or break our emotional state.”
Engaging in behaviors that foster a healthy mental state can create a positive ripple effect that in turn encourages you to continue participating in those activities. This concept is at the root of the popularization of self-care.
“Behavioral activation therapies help reduce depression and anxiety symptoms by activating a reward system, and have been shown to be very effective,” said Bisma Anwar, a licensed therapist with Talkspace. “For example, replacing avoidant behaviors, like staying at home, with more rewarding behaviors, such as meeting up with friends for a walk, can increase a person’s motivation to continue this positive behavior.”
Initially, these actions might feel daunting and require a lot of effort. But if you commit to just giving it a try, you activate the positive reinforcement system.
“When you put one foot in front of the other, voila! You start walking,” said Sue Varma, a clinical assistant professor of psychiatry at NYU Langone Health. “Just like exercising, you may not initially be in the mood, but you end up feeling good afterwards and are glad you did it.”

Another way that behavioral activation can improve mental health is by helping people become more aware of which activities give rise to positive emotions, and which have the opposite effect. A person using this approach might also be reminded that they have the ability to experience joy, and remember how it feels.
“Through intentional tracking, the client improves their ability to recognize positive experiences throughout their day and increases their awareness of cause and effect,” said Marianela Dornhecker, a licensed psychologist practicing in Missouri and Texas. “With this increased awareness, clients typically feel more motivated to engage in those activities, and mindful of avoiding activities that aren’t helpful to them.”

Behavioral activation, which is similar in some ways to the fake it till you make it approach, is often used as a mental health coping strategy.
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DELMAINE DONSON VIA GETTY IMAGES
Behavioral activation, which is similar in some ways to the "fake it till you make it" approach, is often used as a mental health coping strategy.

Is it the same as “fake it till you make it”?

“This technique is often accompanied by the idea of ‘fake it till you make it’ because at the time, you may not feel like doing the things that are part of the behavioral activation, such as going for a walk or planning a nice meal with a friend,” Gitlin said. “The technique asks that you not think too hard about whether or not you genuinely feel like doing something ― i.e. fake it ― and instead focus on completing the task itself.”
In a sense, behavioral activation is like pretending that you feel better. But in doing this positive behavior, you’ll likely develop some positive feelings that can lead to “an upward spiral of motivation,” Gitlin said.

Still, some experts say there are crucial differences.
“There is an aspect of ‘fake it till you make it’ because you’re activating behaviors that don’t necessarily align with your current emotional state or idea of your sense of self,” Thomasian said. “However, I think the difference comes from the intent of the behavior.”
She offered running as an example. Following a pure “fake it till you make it approach,” you would fake being a runner even though you’re a beginner, until you eventually get good at running.
“In behavioral activation, there is a different end to the means,” Thomasian said ― it’s more like “I’m going to start running even though it’s the last thing I want to do, because doing so will help my emotional state.”
Besides, if you think of behavioral activation as “faking” your motivation to do an activity, it could affect your intentions and make the technique less likely to work.
“‘Faking it’ implies forced action, a lack of authenticity, connection and a cynicism around an experience,” said Monica Vermani, a Toronto-based clinical psychologist and author of “A Deeper Wellness: Conquering Stress, Mood, Anxiety, and Traumas.” “Framing it as a route or path to betterment, self-improvement, healing, overcoming anxiety and fears, and self-actualization creates a more positive and enjoyable process and experience ― which can help conquer maladaptive patterns.”

Dornhecker believes a better way to think about the mechanism of behavioral activation is the idea that “energy begets energy.”
“When someone is experiencing depression, their brain can feel like it is in a fog, or everything feels ‘underwater’ or dulled out, which can lead to low activity,” she explained. “This low activity actually has the effect of creating even lower energy and decreasing motivation. However, when someone makes the decision to do an activity that requires energy (even if they don’t feel like it), this actually has the effect of creating more energy in the body and thus increasing motivation and mood.”

How can you implement it?

Behavioral activation can take many forms, but here are some general steps for using this technique.
1. Monitor your actions and feelings.
“The first step of behavioral activation is actively monitoring,” said Shagoon Maurya, a psychotherapist based in Australia. “It is critical to be fully aware of our daily activities and how they affect our mood.”
You can keep a journal or download an app to take notes about what you’re doing and how you’re feeling. As you track your actions and the emotions they evoke, make a list of the behaviors that make you feel good and commit to implementing them in your everyday life.

“If you’re unsure what behaviors to focus on, it can be helpful to consider one’s values,” said Sanam Hafeez, a neuropsychologist in New York. “Your values are what matter most to you, and can guide how you live or how you’d like to live. You can ask yourself: ‘What would my life be like if I had no obstacles?’ ‘What matters most to me?’ ‘Who do I look up to? What qualities do they encompass?’”
Once you’ve determined which activities improve your mood and give you a sense of purpose, challenge yourself to do them more, even if you can’t always find the motivation.
“Repetition is key,” Vermani said. “You want to become bored by what makes you anxious, apprehensive and uncomfortable. The more you do something, the less intimidating and threatening that activity feels. The less threatening an activity becomes, the less power cognitive distortions and maladaptive thoughts [have].”
2. Set achievable goals for positive behaviors.
Vermani recommends setting achievable goals by focusing on one or two behaviors at a time and practicing them on a regular basis.
“For example, a person who has difficulty getting out of bed could commit to putting on an outfit that makes them feel good every morning, even if they do not go out anywhere, or commit to setting their alarm to play their favorite music to motivate them to get out of bed,” she said. “The goal here is to create something that elevates and improves your mood, lowers your sense of dread and sadness, and limits potential stressors.”

Eventually, you can build up to bigger activities like organizing a social gathering or pursuing a major project at work.
3. Minimize the negative behaviors.
As you identify and implement the behaviors that positively impact your mood, you should also take note of which ones don’t bring you joy or fulfillment.
“Reduce behaviors that make you feel bad,” Vermani said. “For example, someone may choose to limit the amount of time they spend on social media, and replace this with connecting one-on-one with friends. By getting rid of unneeded and unhelpful behaviors, you can increase self-esteem and self-confidence.”
4. Don’t confuse behavioral activation with busyness.
“Behavioral activation can sometimes be misunderstood to mean that being busy is the way to combat depression,” Dornhecker said. “Busyness for busyness’ sake is not what helps someone feel motivated ― in fact, this can lead to burnout.”
She noted that some of the activities that are valuable in combating mental health symptoms involve being busy ― for instance, learning a new skill. But other helpful activities can be slow and relaxing, like spending time outside or sipping coffee as you listen to music.

5. Use the technique in combination with other coping strategies.
Remember that behavioral activation is just one of many tools involved in cognitive behavioral therapy. It doesn’t necessarily work for everyone, and that’s OK.
“Although some people may respond well to behavioral changes alone, others may need a mixture of therapies to help,” Vermani said. “When behavioral activation alone does not help with a person’s symptoms, a mental health professional may be able to treat the condition more holistically in partnership with their medical team.”


 

'Fake It Till You Make It' Isn't Just A Cliché. It's Backed By Science.​

The concept is more formally called "behavioral activation." Here's how it can help your mental health.

The phrase “fake it till you make it” can feel like a cliché, but there’s some value to this idea in the mental health field.
The expression is often evoked in describing the concept of behavioral activation ― a useful tool in managing conditions like depression and anxiety. But what exactly is this approach, and how does it compare to the idea of “faking” confidence, competence or positive emotions in order to achieve results?



Very proactive, I predict backlash from big pharm
 
Restoration of function in organs of pigs dead for an hour challenges our ideas of death

In the work, published on 3 August in Nature, researchers connected pigs that had been dead for one hour to a system called OrganEx that pumped a blood substitute throughout the animals’ bodies. The solution — containing the animals’ blood and 13 compounds such as anticoagulants — slowed the decomposition of the bodies and quickly restored some organ function, such as heart contraction and activity in the liver and kidney. Although OrganEx helped to preserve the integrity of some brain tissue, researchers did not observe any coordinated brain activity that would indicate the animals had regained any consciousness or sentience.​
Sestan’s team obtained pigs from a local farm breeder and monitored them for three days before sedating them, putting them on a ventilator and inducing cardiac arrest by delivering a shock to their hearts. After confirming a lack of pulse, they removed the animals from the ventilators. One hour after the pigs died, they restarted the ventilators and anaesthesia. Some of the pigs were then attached to the OrganEx system; others received no treatment or were hooked up to an extracorporeal membrane oxygenation (ECMO) machine, which some hospitals use in a last-ditch effort to supply oxygen to and remove carbon dioxide from the body.​
After six hours, the researchers noticed that circulation had restarted much more effectively in pigs that received the OrganEx solution than in those that received ECMO or no treatment. Oxygen had begun flowing to tissues all over the bodies of the OrganEx animals, and a heart scan detected some electrical activity and contraction. But the heart had not fully restarted, and it’s unclear what exactly it was doing in those animals, says David Andrijevic, a neuroscientist at Yale University and team member.​
The researchers also noticed that the livers of the OrganEx pigs produced much more of a protein called albumin than did the livers of pigs in the other groups. And cells in each of the vital organs of the OrganEx pigs responded to glucose much more than did the animals in the other groups, suggesting that the treatment had kick-started metabolism.​
The researchers also found that more genes responsible for cellular function and repair were active across all major organs in the OrganEx group compared with the ECMO or no-treatment groups.​
The latest experiments are “stunning”, says Nita Farahany, a neuroethicist at Duke University in Durham, North Carolina. Although this study is preliminary, she says it suggests that some perceived limitations of the human body might be overcome in time.​
As with the 2019 paper, the study is likely to reinvigorate a debate about the definition of death and the ethics of post-mortem organ donation. The authors warn that these results do not show that the pigs have somehow been reanimated after death, especially in the absence of electrical activity in the brain. “We made cells do something they weren’t able to do” when the animals were dead, says team member Zvonimir Vrselja, a neuroscientist at Yale University in New Haven, Connecticut. “We’re not saying it’s clinically relevant, but it’s moving in the right direction.”​
Today, ECMO is deployed mainly as a life-saving intervention for patients with severe heart and lung conditions, but there has been growing interest in using it to preserve organs in people for whom resuscitation has failed. Major advances in perfusion technologies could some day increase the likelihood of physicians being able to resuscitate patients, as commentators noted in 20193. That potential could also make it harder for surgeons to ethically justify the use of perfusion to recover transplantable organs after patients’ hearts or lungs have stopped working.​
The latest findings raise a slew of questions — not least, whether medical and biological determinations of death will need revising. To be better prepared for that possibility, physicians might need to rethink how they are using perfusion systems. Here, I describe current practice. I also lay out what needs to be done differently — both to improve care now, and to ensure that future technologies are used to patients’ benefit, not detriment.​
The study also further emphasizes that death is not a moment but a process, making it challenging to come up with a uniform way to declare a person dead, says Arthur Caplan, a bioethicist at New York University. That means that the legal definition of death will continue to adapt as medicine continues to advance, he adds. “People tend to focus on brain death, but there’s not much consensus on when cardiac death occurs,” he says. “This paper brings that home in an important way.”​
Paper General Writeup Critical-care Writeup

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a, Connection of the porcine body to the OrganEx perfusion system (or ECMO, not shown) through cannulation of the femoral artery and vein. b, Simplified schematic of the OrganEx perfusion device. The system is equipped with a centrifugal pump, pulse generator, haemodiafiltration, gas infusion, drug-delivery systems and sensors to measure metabolic and circulation parameters. c, Schematic of the experimental workflow and conditions. VF, ventricular fibrillation.
Spoiler I think it is obvious that there is more going on in the OrganEx animal :
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a,b, Representative images of abdominal fluoroscopy (a; n = 9) and ophthalmic and renal ultrasound (b; n = 6) after 3 h of perfusion. ECMO is shown at the top and OrganEx is shown at the bottom. c., colour; RI, resistive index. ce, Changes in the total flow rate and brachial arterial pressure (c), the percentage of venous O2 saturation (d) and K+ concentration and pH in the serum (e) throughout the perfusion protocols. n = 6. For ce, data are mean ± s.e.m. Statistical analysis was performed using unpaired two-tailed t-tests; **P < 0.01, ***P < 0.001; NS, not significant. Further detailed information on statistics and reproducibility are provided in the Methods.
 
If you are female and vegetarian, make sure you get enough calcium

The risk of hip fracture in women on plant-based diets is unclear. We aimed to investigate the risk of hip fracture in occasional meat-eaters, pescatarians, and vegetarians compared to regular meat-eaters in the UK Women’s Cohort Study and to determine if potential associations between each diet group and hip fracture risk are modified by body mass index (BMI).​
Amongst 26,318 women, 822 hip fracture cases were observed (556,331 person-years). After adjustment for confounders, vegetarians (HR (95% CI) 1.33 (1.03, 1.71)) but not occasional meat-eaters (1.00 (0.85, 1.18)) or pescatarians (0.97 (0.75, 1.26)) had a greater risk of hip fracture than regular meat-eaters. There was no clear evidence of effect modification by BMI in any diet group (p-interaction = 0.3).​
Vegetarian women were at a higher risk of hip fracture compared to regular meat-eaters.​
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Spoiler Legend :
Risk of hip fracture in occasional meat-eaters, pescatarians, and vegetarians compared to regular meat-eaters in the UKWCS. The multivariable-adjusted model was adjusted for the following (all at recruitment): ethnicity (white, Asian, black, other); socio-economic status (professional/managerial, intermediate, routine/manual); marital status (married/living as married, separated/divorced, single/widowed); menopausal status (premenopausal, postmenopausal); number of children (continuous); prevalence of cardiovascular disease, cancer, or diabetes (yes, no); physical activity in hours per day (continuous); smoking status (current, former, never); alcohol consumption (> 1/week, ≤ 1/week, never); BMI (continuous); and any nutritional supplement use (yes, no). HR (95% CI), hazard ratio (95% confidence interval)
 
Thinking hard really does tire out the brain

It’s not just in your head: a desire to curl up on the couch after a day spent toiling at the computer could be a physiological response to mentally demanding work, according to a study that links mental fatigue to changes in brain metabolism.​
The study, published on 11 August in Current Biology, found that participants who spent more than six hours working on a tedious and mentally taxing assignment had higher levels of glutamate — an important signalling molecule in the brain. Too much glutamate can disrupt brain function, and a rest period could allow the brain to restore proper regulation of the molecule, the authors note. At the end of their work day, these study participants were also more likely than those who had performed easier tasks to opt for short-term, easily won financial rewards of lesser value than larger rewards that come after a longer wait or involve more effort.​

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Spoiler Legend :
Glutamate was the only metabolite to show the expected three-way interaction (group × region × session).
(A) Data collection. The left lateral prefrontal region (axial slice at the bottom) was defined as the cluster showing reduced activity with cognitive fatigue in a previous fMRI study.24 On top slices are shown the locations of the MRS voxels of interest (VOIs, 35 × 25 × 15 mm) in the primary visual cortex (V1, left) and in the lateral prefrontal cortex (lPFC, right). The lPFC VOI was individually adjusted to cover most of the cluster identified with fMRI, whereas the V1 VOI was placed to cover the medial part of the occipital cortex. The glutamate peak (Glu) is indicated within an example individual spectrum acquired in the lPFC.
(B) Main results from 1H MRS. Top: glutamate concentration levels were normalized over concentrations of total creatine (tCr, shown here), myoinositol (Ins, shown in Figure S2), and total N-acetyl aspartate (tNAA, shown in Figure S2). The three-way interaction (group × region × session) was significant in the three normalized measures. For visual comparison with behavioral measures and model predictions, data were also normalized to the grand mean of the first session. See Figure S3 for additional metabolites. Bottom: main results from diffusion-weighted MRS. Glx (glutamate plus glutamine) were again the only metabolites for which diffusion measures (apparent diffusion coefficients [ADCs], see STAR Methods) showed the expected three-way interaction. Error bars indicate inter-participant standard errors of the mean (SEM). Stars on brackets indicate significant group-by-session interactions.


Writeup Paper
 
Were the dinosaurs killed by two asteroids?

What appears to be a 9 kilometre-wide crater has been discovered buried beneath the sea floor near the coast of West Africa. It was made around the time of the larger Chicxulub impact that wiped out most dinosaurs, leading to speculation that it was caused by a chunk that broke off the Chicxulub asteroid.​
Writeup (possibly paywalled?) Paper

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Spoiler Legend :

Fig. 1. Map and regional seismic sections showing location of Nadir Crater.
(A) Regional bathymetry map of the Guinea Plateau and Guinea Terrace showing location of 2D seismic reflection and well data used in this study. JS, Jane Seamount; NS, Nadir Seamount; PS, Porter Seamount. The white dashed line shows the NE extent of high-amplitude discontinuous seismic facies at the top Maastrichtian interpreted as ejecta deposits and associated tsunami deposits. The north-east limit of this facies closely corresponds with the Maastrichtian shelf-slope break at the landward margin of the Guinea Terrace. Inset map shows a paleogeographic reconstruction of the Atlantic near the end of the Cretaceous, ~66 Ma ago, made using GPlates software (58). Ch, Chicxulub Crater; Nd, Nadir Crater; Bo, Boltysh Crater. (B). Regional composite 2D seismic reflection profile extending from the GU-2B-1 well in the east to the deep Atlantic basin in the west, showing the structural and stratigraphic character of the Guinea Plateau and Guinea Terrace. (C) North-South seismic profile from the salt basin in the north to the Nadir Seamount, south of the Guinea Fracture Zone. Data courtesy of the Republic of Guinea and TGS.


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Spoiler Legend :
Fig. 5. Conceptual model of the impact sequence at the Nadir impact site, based on seismic observations and analog models (6, 7, 21).
(A) At time (t) = 0, the impactor hits the water surface at a velocity of ~20 km/s, initiating a rim-wave tsunami in its wake. (B) Several seconds later, the transient crater forms, as the impactor and a substantial body of water are vaporized. Impactites (melt rock and breccias) line the transient cavity. Tsunami waves propagate away from the evacuated crater. Shock waves cause substantial damage below and around the impact site, and seismic waves propagate across the plateau; (C) major uplift (~400 m relative to preimpact regional) occurs in the “rebound” crater modification phase, resulting in the formation of a raised crater peak; (D) radial collapse of the subsurface damage zone results in further modification of the crater, including the formation of terraces at the surface. Resurge of water transports substantial volume of ejecta and other sediment into the crater, deposited above the impactites.


Spoiler Full writup :
What appears to be a 9 kilometre-wide crater has been discovered buried beneath the sea floor near the coast of West Africa. It was made around the time of the larger Chicxulub impact that wiped out most dinosaurs, leading to speculation that it was caused by a chunk that broke off the Chicxulub asteroid.

“It definitely fits the bill for an impact crater,” says Uisdean Nicholson at Heriot-Watt University in Edinburgh, UK.

Nicholson spotted the feature in seismic reflection data supplied by the oil and gas industry. The likely crater, named the Nadir crater after a nearby seamount, is on the continental shelf a few hundred kilometres off the coast of Guinea, buried beneath around 300 metres of sediment in an area where the water is 900 metres deep.


The structure has all the features characteristic of an impact crater of this size, says Nicholson, including a raised rim and signs of ejected material outside the crater itself. Modelling by team member Veronica Bray at the University of Arizona in Tucson suggests it was caused by the impact of an asteroid around 400 metres in diameter.

The Nadir crater appears to have formed around 66 million years ago, the same time as the 180 kilometre-wide Chicxulub crater in what is now Mexico. That has led the team to speculate that it was made by a chunk that broke off the Chicxulub asteroid, which is estimated to have been 13 kilometres in diameter.

If this had happened just before impact, the two craters would be very close. Instead, Nicholson suggests that gravity could have broken the asteroid apart during an earlier orbit that passed closer to Earth, leading to two impacts within a few days of each other.


This is what happened with the Shoemaker-Levy comet, says Nicholson, which was ripped into fragments by Jupiter’s gravity in 1992 and then struck the planet in 1994. At least 21 fragments hit Jupiter over a six-day period.

It is possible that the Chicxulub asteroid broke up into several fragments too, says Nicholson. Other impact craters may remain to be discovered or could have been destroyed by tectonic processes. Craters don’t form when asteroids hit water several kilometres deep, as most of our oceans are.

“This is an exciting discovery,” says Gareth Collins at Imperial College London, who has studied the Chicxulub impact. “It certainly has lots of features consistent with an impact origin.”

However, Collins isn’t convinced that the event is linked to the Chicxulub impact, pointing out that there is a lot of uncertainty in the dating. “I think that the two events are more likely to be unrelated,” he says.

Nicholson thinks this is a possibility. His team has put in a proposal to drill through the Nadir crater and retrieve cores that will confirm if it is an impact structure and allow the event to be much more precisely dated.

The Nadir impact alone wouldn’t have caused a major extinction, says Nicholson. The event would have mostly affected the surrounding region, not least by creating tsunami waves that would have been 500 metres high near the impact site, according to the study. “It would have been a very significant regional event,” he says.

However, the Nadir asteroid could have triggered some global warming by releasing carbon from the black shale rocks it struck, and also by destabilising methane hydrates on the sea floor.

The Chixculub impact was around 1000 times more powerful and blanketed the entire planet in dust within a few hours. It wiped out all dinosaurs apart from birds and brought the long Cretaceous Period to a decisive end. Palaeontologists have discovered a site in North Dakota that they think contains fossils of animals killed by the impact.
 
It doesn't seem that far-fetched (to me) to suggest that the Nadir crater was created at the same time/by a chunk of the same impactor as the Chixculub crater — if the inital (atmospheric) impact-angle was shallow enough, and/or the airburst-altitude was high enough, it seems rather plausible. At the estimated impact-speed of 20 km/s(!), a broken-off chunk would only have taken 150 seconds (2.5 minutes) to cross 3000 km (i.e. the Atlantic!), and if such a "double-impact" hypothesis turned out to be correct, any competent astrophysicist could probably calculate an entry angle + speed needed for a single atmospheric-entry to make both craters.

(IIRC, the Chixculub meteorite was rich in iridium — the globally distributed iridium-rich layer at ~65.5 mya being one of the factors that clued the original geologists(?) into positing a meteorite-impact-related ELE in the first place. So it might be interesting to investigate whether the debris in the Nadir crater is also richer in iridium than the expected Earth-baseline — and also whether there are any additional impact-craters further SW along the west African continental shelf, along the same approximate line-of-flight)
 

proton contains a charm quark​

The textbook description of a proton says it contains three smaller particles - two up quarks and a down quark - but a new analysis has found strong evidence that it also holds a charm quark

PHYSICS 17 August 2022
By Alex Wilkins

Proton
[/URL]
An artist’s impression of a proton – the large red spheres are up quarks and the large blue sphere a down quark
CERN
The proton, a particle found at the heart of every atom, appears to have a more complicated structure than is traditionally given in textbooks. The find could have ramifications for sensitive particle physics experiments like the Large Hadron Collider (LHC). While protons were once thought to be indivisible, experiments with particle accelerators in the 1960s revealed that they contained three smaller particles, called quarks. Quarks come in six types, or flavours, and the proton contains two up quarks and one down quark.

Could the LHC reveal a new force of nature? Harry Cliff at New Scientist Live this October
But in quantum mechanics, a particle’s structure is governed by probabilities, meaning there is theoretically a chance that other quarks could crop up inside the proton in the form of matter-antimatter pairs. An experiment at the European Muon Collaboration at CERN in 1980 hinted the proton might contain a charm quark and its antimatter equivalent, an anticharm, but the results were inconclusive and hotly debated.


There were further attempts to identify the proton’s charm component, but different groups found conflicting results and had difficulty separating out the intrinsic building blocks of a proton from the high energy environment of particle accelerators, where every kind of quark is created and destroyed in rapid succession.

Now, Juan Rojo at Vrije University Amsterdam in the Netherlands and his colleagues have found evidence that a small part of the proton’s momentum, around 0.5 per cent, comes from the charm quark. “It’s remarkable that even after all these decades of study, we’re still finding new properties of the proton and, in particular, new constituents,” says Rojo. To isolate the charm component, Rojo and his team used a machine learning model to come up with hypothetical proton structures consisting of all the different flavours of quarks and then compared them with more than 500,000 real-world collisions from decades of particle accelerator experiments, including at the LHC.

This use of machine learning was especially important, says Christine Aidala at the University of Washington, because it could generate models that physicists wouldn’t necessarily think of by themselves, reducing the chance of biased measurements. The researchers found that, if the proton doesn’t contain a charm-anticharm quark pair, there is only a 0.3 per cent chance of seeing the results they examined. Physicists call this a “3-sigma” result, which is normally seen as a potential sign of something interesting. More work is needed to boost the results to 5-sigma level, meaning about a 1 in 3.5 million chance of a fluke result, which is traditionally the threshold for a discovery.

The team looked at recent results from the LHCb Z-boson experiment and modelled the statistical distribution of the proton’s momentum both with and without a charm quark. They found the model better matched the results if the proton is assumed to have a charm quark. This means they are more confident in proposing the presence of a charm quark than the sigma level by itself suggests. “The fact that very different studies converge on the same result made us especially confident that our results were solid,” says Rojo.

“Given how ubiquitous this particle is and how long we’ve known about it, there’s still a lot we don’t actually understand about its substructure, so this is definitely important,” says Harry Cliffe at the University of Cambridge.
The proton’s charm component could also have ramifications for other physics experiments at the LHC, says Cliffe, as they rely on accurate models of proton substructure. The IceCube Neutrino Observatory in Antarctica, which looks for rare neutrinos produced when cosmic rays hit particles in Earth’s atmosphere, might also need to take this new structure into account, says Rojo. “The probability of a cosmic ray impacting an atmosphere nucleus and producing neutrinos is quite sensitive to the charm content of the proton,” he says.

Journal reference: Nature, DOI: 10.1038/s41586-022-04998-2
 

proton contains a charm quark​

The textbook description of a proton says it contains three smaller particles - two up quarks and a down quark - but a new analysis has found strong evidence that it also holds a charm quark

PHYSICS 17 August 2022
By Alex Wilkins

Proton
[/URL]
An artist’s impression of a proton – the large red spheres are up quarks and the large blue sphere a down quark
CERN
I could not get my head around this. Are they saying that all protons contain charm quarks, or that it is one of those uncertainty things, in that we cannot say there are exactly zero charm quarks in protons so they sometimes have one?

Brain stimulation leads to long-lasting improvements in memory

People’s ability to remember fades with age — but one day, researchers might be able to use a simple, drug-free method to buck this trend.​
In a study published on 22 August in Nature Neuroscience, Robert Reinhart, a cognitive neuroscientist at Boston University in Massachusetts, and his colleagues demonstrate that zapping the brains of adults aged over 65 with weak electrical currents repeatedly over several days led to memory improvements that persisted for up to a month.​
Previous studies have suggested that long-term memory and ‘working’ memory, which allows the brain to store information temporarily, are controlled by distinct mechanisms and parts of the brain. Drawing on this research, the team demonstrated that stimulating the dorsolateral prefrontal cortex — a region near the front of the brain — with high-frequency electrical currents improved long-term memory, whereas stimulating the inferior parietal lobe, which is further back in the brain, with low-frequency electrical currents boosted working memory.​

Writeup Paper

41593_2022_1132_Fig1_HTML.png

Spoiler Legend :
The theta-rate IPL and gamma-rate DLPFC HD-tACS protocols and corresponding electric field models shown on three-dimensional reconstructions of the cortical surface. The left DLPFC and left IPL were targeted, each protocol using nine electrodes configured in a center-surround, source-sink pattern to achieve maximum focality. The location and current intensity value of each modulating electrode are shown. The DLPFC protocol included (in mA): FP1 (−0.6662), Fz (0.0739), F1 (−0.4438), AF3 (1.5892), FC3 (−0.0048), F5 (−0.2312), AF7 (−0.194), AFz (−0.3744) and EX17 (0.2513). The IPL protocol included (in mA): C3 (−0.2997), T7 (−0.3386), CP1 (−0.2975), FC5 (−0.1284), CP5 (1.5818), FT7 (−0.0852), TP7 (−0.1413), PO7 (−0.2366) and EX13 (−0.0545).

41593_2022_1132_Fig4_HTML.png

Spoiler Legend :
Regression analyses were performed to test for the presence of a linear relationship across participants between the rate of change in recall performance during neuromodulation and the recall performance 1 month after the intervention. a, Scatter plot shows the speed (rate of change) of each participant’s improvement in primacy over 4 days of DLPFC gamma neuromodulation against the same individual’s primacy score 1 month after intervention in Experiment 1. Gray dots show individual participant data (n = 20). The solid line indicates a regression fit, and the error bands show 95% CI. This exploratory analysis identified significant, positive linear relationships between the rate of primacy improvements and 1-month primacy performance in the DLPFC gamma group (r18 = 0.817, P = 1.1 × 10−5). b, Scatter plot as in a for recency in the IPL theta group (n = 20) in Experiment 1. Significant, positive, linear relationship was observed between the rate of recency improvements and 1-month recency performance in the IPL theta group (r18 = 0.655, P = 0.002). These analyses were subjected to Bonferroni correction for multiple comparisons (Pcorr < 0.0125). CI, confidence interval.
 
I could not get my head around this. Are they saying that all protons contain charm quarks, or that it is one of those uncertainty things, in that we cannot say there are exactly zero charm quarks in protons so they sometimes have one?
idk, but I read it to mean that there is a charm quark component to protons and not just the low probability of it. We are dealing with quarks, so we are still figuring things out. If the presence of "charm" in protons is only "sometimes" that it seems to me that stepping into a world where there may be different kinds of protons: charmed and not. Quantum strangeness. :D
 
a world where there may be different kinds of protons: charmed and not
But only when we look at them. Until then they all are in a charmed and not superposition. Not strange at all :crazyeye:
 
NYT paywall.

Your Doppelgänger Is Out There and You Probably Share DNA With Them​

That person who looks just like you is not your twin, but if scientists compared your genomes, they might find a lot in common.

Charlie Chasen and Michael Malone met in Atlanta in 1997, when Mr. Malone served as a guest singer in Mr. Chasen’s band. They quickly became friends, but they didn’t notice what other people around them did: The two men could pass for twins.
Mr. Malone and Mr. Chasen are doppelgängers. They look strikingly similar, but they are not related. Their immediate ancestors aren’t even from the same parts of the world; Mr. Chasen’s forebears hailed from Lithuania and Scotland, while Mr. Malone’s parents are from the Dominican Republic and the Bahamas.

23tb-doppelgangers1b-superJumbo.png


The two friends, along with hundreds of other unrelated look-alikes, participated in a photography project by François Brunelle, a Canadian artist. The picture series, “I’m not a look-alike!,” was inspired by Mr. Brunelle’s discovery of his own look-alike, the English actor Rowan Atkinson.

The project has been a hit on social media and other parts of the internet, but it’s also drawn the attention of scientists who study genetic relationships. Dr. Manel Esteller, a researcher at the Josep Carreras Leukaemia Research Institute in Barcelona, Spain, had previously studied the physical differences between identical twins, and he wanted to examine the reverse: people who look alike but aren’t related. “What’s the explanation for these people?” he wondered.

The whole story and the science behind it is here:
 
I wouldn't be surprised if there isn't an app for finding lookalikes coming soon (searching fb, Instagram, etc w an algorithm)
 
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