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Novel Genetic Patterns May Make Us Rethink Biology and Individuality - The Almagest

Novel Genetic Patterns May Make Us Rethink Biology and Individuality - The Almagest | Amazing Science | Scoop.it

Professor of Genetics Scott Williams, PhD, of the Institute for Quantitative Biomedical Sciences (iQBS) at Dartmouth’s Geisel School of Medicine, has made two novel discoveries: first, a person can have several DNA mutations in parts of their body, with their original DNA in the rest—resulting in several different genotypes in one individual—and second, some of the same genetic mutations occur in unrelated people. We think of each person’s DNA as unique, so if an individual can have more than one genotype, this may alter our very concept of what it means to be a human, and impact how we think about using forensic or criminal DNA analysis, paternity testing, prenatal testing, or genetic screening for breast cancer risk, for example. Williams’ surprising results indicate that genetic mutations do not always happen purely at random, as scientists have previously thought. His work, done in collaboration with Professor of Genetics Jason Moore, PhD, and colleagues at Vanderbilt University, was published in PLOS Genetics journal.[1]


Genetic mutations can occur in the cells that are passed on from parent to child and may cause birth defects. Other genetic mutations occur after an egg is fertilized, throughout childhood or adult life, after people are exposed to sunlight, radiation, carcinogenic chemicals, viruses, or other items that can damage DNA. These later or “somatic” mutations do not affect sperm or egg cells, so they are not inherited from parents or passed down to children. Somatic mutations can cause cancer or other diseases, but do not always do so. However, if the mutated cell continues to divide, the person can develop tissue, or a part thereof, with a different DNA sequence from the rest of his or her body.


“We are in reality diverse beings in that a single person is genetically not a single entity—to be philosophical in ways I do not yet understand—what does it mean to be a person if we are variable within?” says Williams, the study’s senior author, and founding Director of the Center for Integrative Biomedical Sciences in iQBS. “What makes you a person? Is it your memory? Your genes?” He continues, “We have always thought, ‘your genome is your genome.’ The data suggest that it is not completely true.”


In the past, it was always thought that each person contains only one DNA sequence (genetic constitution). Only recently, with the computational power of advanced genetic analysis tools that examine all the genes in one individual, have scientists been able to systematically look for this somatic variation. “This study is an example of the type of biomedical research project that is made possible by bringing together interdisciplinary teams of scientists with expertise in the biological, computational and statistical sciences.” says Jason Moore, Director of the iQBS, who is also Associate Director for Bioinformatics at the Cancer Center, Third Century Professor, and Professor of Community and Family Medicine at Geisel.


Having multiple genotypes from mutations within one’s own body is somewhat analogous to chimerism, a condition in which one person has cells inside his or her body that originated from another person (i.e., following an organ or blood donation; or sometimes a mother and child—or twins—exchange DNA during pregnancy. Also, occasionally a person finds out that, prior to birth, he or she had a twin who did not survive, whose genetic material is still contained within their own body).[2] Chimerism has resulted in some famous DNA cases: one in which a mother had genetic testing that “proved” that she was unrelated to two of her three biological sons.[3]


As suggested by Maria Schnee (newphoenix.info)


1 Williams, Scott, et al., Recurrent tissue-specific mtDNA mutations are common in humans. http://www.plosgenetics.org/doi/pgen.1003929.


2 Strain L, Dean JC, Hamilton MP, Bonthron D. A true hermaphrodite chimera resulting from embryo amalgamation after in vitro fertilization. N Engl J Med 1998;(338):166-9/


3 Norton AT and Zehner O. Project MUSE: Today’s Research, Tomorrow’s Inspiration. http://www.academia.edu.

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Unlimited, at-home coronavirus testing for your organization | Amazing Science | Scoop.it

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Most of Europe’s mighty rivers are drying up due to the climate-driven drought

Most of Europe’s mighty rivers are drying up due to the climate-driven drought | Amazing Science | Scoop.it

From the Loire to the Danube, dried-out rivers are jeopardizing Europe's trade, transport, energy and wildlife.

 

Europe’s major rivers are shrinking under the most severe climate-driven drought in decades. It’s distressing enough to see mighty waterways like the Loire, Po and Rhine reduced to a trickle in places.  But the ongoing drought is also revealing how much we depend on them for trade, energy and transport. The Rhine’s evaporation is especially concerning. At the chokepoint of Kaub, near Frankfurt, it is expected to fall below 40cm on Friday. This would make it impassable for some larger ships carrying supplies of oil, coal and gas. 

 

German power plants are particularly dependent on the deliveries as Russia restricts gas flow, and the drought could compound the country’s energy crisis. France, which uses the most nuclear energy in the EU, has also recently run into hot water on the Rhône and Garonne rivers. This week, electricity utility company EDF had to reduce output at some of its power stations as temperatures were too high to use river water to cool the plants down.

 

Meanwhile shocking photos of the Loire near its mouth at Nantes yesterday show far more river bed than water, with an essentially redundant bridge to the Loireauxence commune. Across Europe, here’s how photographers have been documenting the devastating impact of heatwaves and drought on most waterways.

 

Flowing from the Swiss Alps, carving much of the Franco-German border, defining the German Rhineland and careering into the Netherlands before reaching the North Sea, the Rhine is a formative part of Europe.  As well as threatening shipping routes in Germany, its current low levels are causing problems for house boat owners on distributary branches, such as on the Netherlands' Waal River.

 

Italy's longest river, the Po, has been struggling to retain its width during the northern region's worst drought in 70 years. Water has already completely disappeared from some tributaries - upstream of Turin for example. The river provides irrigation for nearly a third of Italy's agricultural production. "The future of the harvest is uncertain," Giovanni Daghetta, who owns a 325-hectare rice farm in the province of Pavia, told Euronews last month. "What is certain is that if this drought persists it will do enormous damage."

 

Drought has not been formally declared in England yet - that decision rests with the Environment Agency - but the country has just experienced its driest July since 1935. The source of the Thames has dried up for the first time, experts confirmed last week, moving more than five miles downstream from its original starting point in Gloucestershire.  Thames Water, which provides water to large parts of southeast England,  is the latest utility company to announce a hosepipe ban.

 

The water level of the Danube near Budapest has dropped by 1.5 meters in the last three weeks, and rain isn't expected any time soon. Rising water temperatures in Europe's second-longest river have also been worrying experts. It reached more than 25C for seven days in the Upper Palatinate region of Bavaria.  River heating can cause oxygen to drop beyond survivable levels for fish, and concerns have been raised for the Danube's trout. 

 

A prolonged dry spell and heatwave made last July the hottest month in Spain since records started in 1961. These extreme conditions left Spanish reservoirs at just 40 per cent of capacity on average in early August, well below the ten-year average of around 60 per cent, official data shows. Some rural villages in the northeast of the country were left with drinking water for just 4 hours a day. 

 

With an early heatwave in June and an unusually hot and dry month of May, the bed of the Loire has reached a lower level than usual. Water levels are so low that the river can be crossed on foot in certain places. Two-thirds of the country is at a crisis level for drought. Four recent heatwaves have triggered weeks of wildfires and reduced the mighty Loire to a stream in some stretches. Last week, the government said 100 villages across France were without safe tap water. The Loire river is so low it can be crossed by foot where it used to meet the Allier River at le Bec d’Allier, Cuffy, 9 August, 2022.

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BioGlue: Using sound and bubbles to make bandages stickier and longer lasting

BioGlue: Using sound and bubbles to make bandages stickier and longer lasting | Amazing Science | Scoop.it

Researchers have discovered that they can control the stickiness of adhesive bandages using ultrasound waves and bubbles. This breakthrough could lead to new advances in medical adhesives, especially in cases where adhesives are difficult to apply such as on wet skin.

 

"Bandages, glues, and stickers are common bioadhesives that are used at home or in clinics. However, they don't usually adhere well on wet skin. It's also challenging to control where they are applied and the strength and duration of the formed adhesion," says McGill University Professor Jianyu Li, who led the research team of engineers, physicists, chemists, and clinicians.

 

"We were surprised to find that by simply playing around with ultrasonic intensity, we can control very precisely the stickiness of adhesive bandages on many tissues," says lead author Zhenwei Ma, a former student of Professor Li and now a Killam Postdoctoral Fellow at the University of British Columbia.

 

Ultrasound induced bubbles control stickiness

In collaboration with physicists Professor Outi Supponen and Claire Bourquard from the Institute of Fluid Dynamics at ETH Zurich, the team experimented with ultrasound induced microbubbles to make adhesives stickier. "The ultrasound induces many microbubbles, which transiently push the adhesives into the skin for stronger bioadhesion," says Professor Supponen. "We can even use theoretical modeling to estimate exactly where the adhesion will happen."

 

Their study, published in the journal Science, shows that the adhesives are compatible with living tissue in rats. The adhesives can also potentially be used to deliver drugs through the skin. "This paradigm-shifting technology will have great implications in many branches of medicine," says University of British Columbia Professor Zu-hua Gao. "We're very excited to translate this technology for applications in clinics for tissue repair, cancer therapy, and precision medicine."

 

"By merging mechanics, materials and biomedical engineering, we envision the broad impact of our bioadhesive technology in wearable devices, wound management, and regenerative medicine," says Professor Li, who is also a Canada Research Chair in Biomaterials and Musculoskeletal Health.

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China Approves First Homegrown COVID Antiviral, the HIV drug Azvudine from Genuine Biotech

China Approves First Homegrown COVID Antiviral, the HIV drug Azvudine from Genuine Biotech | Amazing Science | Scoop.it

China’s drug regulator has granted conditional authorization for an HIV drug to be used to treat COVID-19.  China’s drug regulator granted conditional approval on Monday for an HIV drug to be used to treat COVID-19. The drug, Azvudine, developed by Chinese drugmaker Genuine Biotech, is the first oral antiviral for the disease made in China.

 

Genuine Biotech, headquartered in Pingdingshan, applied for regulatory approval earlier this month. The company said that 40% of people with COVID-19 who were given Azvudine for a week in a phase III clinical trial showed “improved clinical symptoms”, compared with 11% of those given a placebo. However, detailed data from the trial, including whether the treatment reduced the risk of hospitalization or death, have not been released yet.

 

Although drug-efficacy data are currently lacking, Jun Wang, a pharmacologist at Rutgers University in New Brunswick, New Jersey, says because Azvudine is already approved in China as an HIV treatment, it should have abundant safety data, which could have fast-tracked its application. Genuine Biotech will need to submit however, more post-marketing data in order for the drug to receive full approval. Most antivirals target two SARS-CoV-2 proteins that are essential for viral replication, a polymerase and a protease. Azvudine tricks the virus polymerase into incorporating the drug into its RNA, which stops the virus from replicating1.

 

In China and globally, the demand for efficient and affordable COVID-19 therapies is enormous, says Sheng Ding, a pharmaceutical chemist at Tsinghua University in Beijing. Until the Azvudine authorization, China had approved only one oral antiviral to treat the disease, Paxlovid, developed by Pfizer in New York City. It is highly effective — it reduces the risk of hospitalization and death by nearly 89% — but supplies in China are very limited. “The market will have room for several more drugs that may not outperform Paxlovid, but allow more people to access effective therapies,” adds Ding. Another Chinese-made oral antiviral, VV116, is in the final stages of development, and another dozen are in various stages of development.

Oral remdesivir

The developers of VV116, Shanghai Junshi Biosciences, plan to seek regulatory approval soon. VV116 is essentially a pill version of the intravenous drug remdesivir, made by Gilead Sciences in Foster City, Ca., and the first drug approved by the US Food and Drug Administration for treating COVID-19. Shanghai Junshi Biosciences slightly tweaked the remdesivir formula and was granted a patent to manufacture it as a pill. It is already being used in Uzbekistan. A phase III trial of VV116 in China compared its effectiveness and safety with that of Paxlovid. The company says that people with COVID-19 who received VV116 had their symptoms alleviated faster and tested negative sooner than those given Paxlovid, but detailed data from the trial have not yet been released. A small peer-reviewed trial involving 136 participants suggested the drug could reduce the period between the first positive COVID-19 test result and the first negative result to 8.5 days, compared with 11 days for those who received a placebo. But scientists say it is unclear how effective the drug is at reducing the risk of hospitalization and death. Wang says he expects VV116 to work to some extent, but it’s unclear whether it will outperform Paxlovid. VV116 also blocks viral replication and, like Azvudine and Paxloivd, works best when taken soon after infection. Scientists say it is difficult to assess the efficacy of Azvudine and VV116 because no detailed data from their phase III trials have been released. “With very limited data, I can’t really tell which one is better,” says Ding, who also leads a team at the non-profit Global Health Drug Discovery Institute, based in Beijing. That team is working on an experimental antiviral for COVID-19, expected to enter clinical trials later this year. Unlike most countries, China continues to implement its strict ‘zero-COVID’ policy, which involves measures such as mass testing and strict quarantine to quash all infections. The approval of effective COVID-19 antivirals probably will not change that policy, Wang says. But Hongtao Yu, a biologist at Westlake University in Hangzhou, China, who is also developing an experimental COVID-19 treatment that might soon enter clinical trials, says that could change if the country can build up a “large stockpile of these pills, which are made very affordable, we can make sure the drugs are widely available in hospitals and pharmacies for the vulnerable. That’s when I think China is ready to open up.”

 

Published in Nature  (July 26, 2022):

https://doi.org/10.1038/d41586-022-02050-x


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What Can AI Tell Us About Our Own Human Intelligence?

What Can AI Tell Us About Our Own Human Intelligence? | Amazing Science | Scoop.it

Can deep learning systems learn to manipulate symbols? The answers might change our understanding of how intelligence works and what makes humans unique.

 

If there is one constant in the field of artificial intelligence it is exaggeration: There is always breathless hype and scornful naysaying. It is helpful to occasionally take stock of where we stand. The dominant technique in contemporary AI is deep learning (DL) neural networks, massive self-learning algorithms which excel at discerning and utilizing patterns in data. Since their inception, critics have prematurely argued that neural networks had run into an insurmountable wall — and every time, it proved a temporary hurdle.

 

In the 1960s, they could not solve non-linear functions. That changed in the 1980s with backpropagation, but the new wall was how difficult it was to train the systems. The 1990s saw a rise of simplifying programs and standardized architectures which made training more reliable, but the new problem was the lack of training data and computing power.

 

In 2012, when contemporary graphics cards could be trained on the massive ImageNet dataset, DL went mainstream, handily besting all competitors. But then critics spied a new problem: DL required too much hand-labeled data for training. The last few years have rendered this criticism moot, as self-supervised learning has resulted in incredibly impressive systems, such as GPT-3, which do not require labeled data.

 

Today’s seemingly insurmountable wall is symbolic reasoning, the capacity to manipulate symbols in the ways familiar from algebra or logic. As we learned as children, solving math problems involves a step-by-step manipulation of symbols according to strict rules (e.g., multiply the furthest right column, carry the extra value to the column to the left, etc.).

 

Gary Marcus, author of “The Algebraic Mind” and co-author (with Ernie Davis) of “Rebooting AI,” recently argued that DL is incapable of further progress because neural networks struggle with this kind of symbol manipulation. By contrast, many DL researchers are convinced that DL is already engaging in symbolic reasoning and will continue to improve at it.

 

At the heart of this debate are two different visions of the role of symbols in intelligence, both biological and mechanical: One holds that symbolic reasoning must be hard-coded from the outset and the other holds it can be learned through experience, by machines and humans alike. As such, the stakes are not just about the most practical way forward, but also how we should understand human intelligence — and, thus, how we should pursue human-level artificial intelligence.

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Light microscopic resolution: how low can you go?

Light microscopic resolution: how low can you go? | Amazing Science | Scoop.it
Classically, light microscopes limits are in the micrometer range. Advances in single-molecule localization microscopy allow for nanometer resolution.

 

Improving the resolution of optical microscopes was thought to be limited by a theorem put forward in the 19th century. However, scientists have been able to overcome this issue in the 21stcentury.

 

 

In the 16-17th century Europe, a Dutch tradesman and scientist named Antoine van Leeuwenhoek used microscopes to discover red blood cells and to first see living sperm cells of animals. In 1873, there was an equation published by Ernst Abbe demonstrating how the resolution of a light microscope was limited by, among other things, the wavelength of light. Through the 19th and much of the 20th century this limit, Abbe’s Limit (0.2 um), was thought to be unsurpassable. However, in 2014, the Nobel Prize in Chemistry was awarded for a technique called single-molecule localization microscopy (SMLM) which bypasses Abbe’s diffraction limit and set a new precedent for the field of microscopy—resolution at the nanoscale level. Today, SMLM approaches have the potential to capture natural processes at the nanoscale level such as molecular complexes, protein-protein interactions, and spatial organizations.

 

A recent work by Coelho et al. leverages this technique, improves upon it, and uses it to look closely at an immune cell called a T cell. The two primary super resolution techniques are stochastic optical reconstruction microscopy (STORM) and DNA point accumulation for imaging in nanoscale topography (DNA-PAINT). In SMLM, single fluorophores are temporally separated by using a weak light pulse to activate a fraction of all the fluorophores. These fluorophores glow until bleached at which point the process is repeated for a new set of fluorophores. Next, the blurry images are mathematically processed using probability theory (i.e. where is the original point source of the light?) to render them much sharper into points. Eventually every frame is superimposed to form one final, super resolution image. However, the time required to sequential image all the individual fluorophores require long acquisition times, as typically tens of thousands of frames are needed to map a given protein species in a cell. Drift during camera exposure affects the localization precision and the accuracy of localization. Thus, in practice the resolution is reduced to tens of nanometers making it unfeasible to conduct distance measurements on biological relevant scales.

 

Coelho et al. overcome this issue using an engineering solution coined Feedback SMLM, “…which can capture molecular emissions in a complex and unknown cellular environment with equal probability and high precision.” In other words, their technique can measure distances between two proteins in a wide range of sample formats, including intact cells, to capture heterogeneity as well as rare events with nanometer resolution.

Feedback SMLM uses three types of corrections: stage-sample feedback loop, autonomous optical feedback loop and piezoelectric mirror correction. Stage-sample feedback is accomplished by using non-fluorescent fiducials (reference points) outside of the field of view. A camera operating at a speed of 370 frames per second tracks the fiducials to provide information of both x-y and position. Stage corrections can happen during sample acquisition with stabilization of 0.4 and 1 nm (SD) in the lateral (x-y) and axial (z) directions, respectively, over hours and days. Optical feedback uses a white LED integrated in the microscope body, creating an optical fiducial, which a camera is monitoring with a precision of 0.05 nm. Finally, the piezoelectric mirror tracks the mechanical instabilities and reduces image drift to 0.22 nm. The mirror correction accomplishes something other SMLM techniques can not; that is the stability of fluorescence path does not have to be computationally corrected post-acquisition.

Using DNA-PAINT with Feedback SMLM the authors generate an ultrahigh resolution image of F-actin. F-actin is an abundant protein in cells and used as an imaging benchmark because the width of actin is sub diffraction limit (i.e <0.2 um). Incredibly an individual actin fibril can be accurately measured to width of 5 to 9 nm without any post-acquisition processing. Electron microscopy measurements corroborate these results. In contrast other current SMLM imaging approaches, e.g. dSTORM, were only able to obtain an approximate width of 20 nm due to insufficient localization precision.

 

Finally, the authors apply their technique to an unanswered immunological question: how do T cells (derived from the Thymus) signal to become activated? T cells activate through their T cell receptor (TCR) which recognizes peptides presented in major histocompatibility complex (pMHC). T cells are exquistively sensitive and can recognize fewer than 10 agonist pMHC ligands with only a few TCRs. The current model suggests a phosphorylation cascade on associated protein dimers (i.e. CD3 dimers) of the TCR triggers cellular activation. It is widely assumed TCR triggering requires the exclusion of the transmembrane phosphatase CD45 to successfully activate. However, these delicate events have never been visualized before and are currently readout biochemically. Coelho et al. activated Jurkat T cells using pMHC coated on a lipid bilayer glass slide. The authors applied Feedback SMLM and DNA-PAINT to monitor CD45 and phosphorylated CD3ζ (pCD3ζ). What they found was spatially separated nano-clusters of pCD3ζ and CD45 at median distances of 19.6 nm. On resting T cells CD3 and CD45 appeared intermix with mean distances of 12.5 nm. Thus, if spatial separation was the means of TCR triggering, the TCR is exquisitely sensitive to 4- to 7-nm differences between CD3 and CD45. Through careful microscopy image analysis, the author's feedback SMLM has provided the means to answer a question previously unknown due to technological reasons and provides new insights into the field of T cell biology.

­

Reference

1) Coelho et al. Ultraprecise single-molecule localization microscopy enables in situ distance measurements in intact cells. Science Advances. Vol 6, Issue 16. 2020. DOI: 10.1126/sciadv.aay8271

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Stability AI launched Stable Diffusion

Stability AI launched Stable Diffusion | Amazing Science | Scoop.it

Github Stable Diffusion is here

 

Stability AI and collaborators are proud to announce the first stage of release of Stable Diffusion to researchers via this form, the model weights are hosted by Hugging Face once you get access. The code is available here and the model card here. A public release is coming soon. Stable Diffusion is a text-to-image model that will empower billions of people to create stunning art within seconds. 

 

The effort has been led by Patrick Esser from Runway and Robin Rombach from the CompVis lab at Heidelberg University (now the Machine Vision & Learning research group at LMU), combined with support from communities at Eleuther AI, LAION and Stability AI's own generative AI team.

 

Stable Diffusion is a breakthrough in speed and quality meaning that it can run on consumer GPUs. You can see some of the amazing output that has been created by this model without pre or post-processing on this page. The model itself builds upon the work of the team at CompVis and Runway in their widely used latent diffusion model combined with insights from the conditional diffusion models by our lead generative AI developer Katherine Crowson, Dall-E 2 by Open AI, Imagen by Google Brain and many others. 

 

Stability AI is delighted that AI media generation is a cooperative field and hope it can continue this way to bring the gift of creativity to all. The core dataset was trained on LAION-Aesthetics, a soon to be released subset of LAION 5B. LAION-Aesthetics was created with a new CLIP-based model that filtered LAION-5B based on how “beautiful” an image was, building on ratings from the alpha testers of stable diffusion. LAION-Aesthetics will be released with other subsets in the coming days on https://laion.ai.

 

Stable diffusion runs on under 10 GB of VRAM on consumer GPUs, generating images at 512x512 pixels in a few seconds. This will allow both researchers and soon the public to run this under a range of conditions, democratizing image generation. The AI researchers around Stability AI look forward to the open ecosystem that will emerge around this and further models to truly explore the boundaries of latent space.

 

The model was trained on an 4,000 A100 Ezra-1 AI ultra-cluster over the last month as the first of a series of models exploring this and other approaches. Stability AI has been testing the model at scale with over 10,000 beta testers that are creating 1.7 million images a day. 

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Bacteria Power a Truly Green Revolution Making Electricity from Human Sweat

Bacteria Power a Truly Green Revolution Making Electricity from Human Sweat | Amazing Science | Scoop.it

Researchers at the University of Massachusetts Amherst recently announced that they have figured out how to engineer a biofilm that harvests the energy in evaporation and converts it to electricity. This biofilm, which was announced in Nature Communications, has the potential to revolutionize the world of wearable electronics, powering everything from personal medical sensors to personal electronics. “This is a very exciting technology,” says Xiaomeng Liu, graduate student in electrical and computer engineering in UMass Amherst’s College of Engineering and the paper’s lead author. “It is real green energy, and unlike other so-called ‘green-energy’ sources, its production is totally green.”

 

That’s because this biofilm—a thin sheet of bacterial cells about the thickness of a sheet of paper—is produced naturally by an engineered version of the bacteria Geobacter sulfurreducens which is known to produce electricity and has been used previously in “microbial batteries” to power electrical devices. But such batteries require that G. sulfurreducens is properly cared for and fed a constant diet. By contrast, this new biofilm, which can supply as much, if not more, energy than a comparably sized battery, works, and works continuously, because it is dead. And because it’s dead, it doesn’t need to be fed.

 

“It’s much more efficient,” says Derek Lovley, Distinguished Professor of Microbiology at UMass Amherst and one of the paper’s senior authors. “We’ve simplified the process of generating electricity by radically cutting back on the amount of processing needed. We sustainably grow the cells in a biofilm, and then use that agglomeration of cells. This cuts the energy inputs, makes everything simpler and widens the potential applications.”

 

The secret behind this new biofilm is that it makes energy from the moisture on your skin. Though we daily read stories about solar power, at least 50% of the solar energy reaching the earth goes toward evaporating water. “This is a huge, untapped source of energy,” says Jun Yao, professor of electrical and computer engineering at UMass, and the paper’s other senior author. Since the surface of our skin is constantly moist with sweat, the biofilm can “plug-in” and convert the energy locked in evaporation into enough energy to power small devices.

 

“The limiting factor of wearable electronics,” says Yao, “has always been the power supply. Batteries run down and have to be changed or charged. They are also bulky, heavy, and uncomfortable.” But a clear, small, thin flexible biofilm that produces a continuous and steady supply of electricity and which can be worn, like a Band-Aid, as a patch applied directly to the skin, solves all these problems.

 

What makes this all work is that G. sulfurreducens grows in colonies that look like thin mats, and each of the individual microbes connects to its neighbors through a series of natural nanowires. The team then harvests these mats and uses a laser to etch small circuits into the films. Once the films are etched, they’re sandwiched between electrodes and finally sealed in a soft, sticky, breathable polymer that you can apply directly to your skin. Once this tiny battery is “plugged in” by applying it to your body, it can power small devices.

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AI generated sequence-based global map of regulatory activity for deciphering human genetics

AI generated sequence-based global map of regulatory activity for deciphering human genetics | Amazing Science | Scoop.it

Epigenomic profiling has enabled large-scale identification of regulatory elements, yet we still lack a systematic mapping from any sequence or variant to regulatory activities. Researchers now address this challenge with Sei, a framework for integrating human genetics data with sequence information to discover the regulatory basis of traits and diseases. Sei learns a vocabulary of regulatory activities, called sequence classes, using a deep learning model that predicts 21,907 chromatin profiles across >1,300 cell lines and tissues.

 

Sequence classes provide a global classification and quantification of sequence and variant effects based on diverse regulatory activities, such as cell type-specific enhancer functions. These predictions are supported by tissue-specific expression, expression quantitative trait loci and evolutionary constraint data. Furthermore, sequence classes enable characterization of the tissue-specific, regulatory architecture of complex traits and generate mechanistic hypotheses for individual regulatory pathogenic mutations. Sei is provided as a resource to elucidate the regulatory basis of human health and disease. Sei is a new framework for integrating human genetics data with a sequence-based mapping of predicted regulatory activities to elucidate mechanisms contributing to complex traits and diseases.

 

Deciphering how regulatory functions are encoded in genomic sequences is a major challenge in understanding how genome variation links to phenotypic traits. Cell type-specific regulatory activities encoded in elements such as promoters, enhancers and boundary elements are critical to defining the complex expression programs essential for multicellular organisms. Most disease-associated variants from genome-wide association studies (GWAS) are located in noncoding regions1, yet without knowing how changes in sequence affect regulatory activities, we cannot predict the impact of these variants and uncover the regulatory mechanisms contributing to complex diseases and traits.

 

Substantial progress has been made in the experimental profiling and integrative analysis of epigenomic marks, such as histone marks and DNA accessibility, across a wide range of tissues and cell types2,3,4. At the same time, deep learning sequence modeling techniques have been successfully applied to learn sequence features predictive of transcription factor (TF) binding and histone modifications5,6,7,8,9,10,11. These models are powerful tools for inferring the impact of sequence variation at the chromatin level—for example, whether a variant increases or decreases C/EBPβ binding. However, we continue to lack an integrative view of sequence regulatory activities, including all major aspects of cis-regulatory functions, such as tissue-specific or broad enhancer and promoter activities. This limits our ability to interpret the integrated effects of all chromatin-level perturbations caused by genomic variants and determine their impact on human health and diseases.

 

The researchers address this challenge by creating a global map for sequence regulatory activity based on a new deep learning-based framework called Sei. This framework introduces a sequence model that predicts 21,907 publicly available chromatin profiles—the broadest set to date—and uses the model to quantitatively characterize regulatory activities for any sequence with a vocabulary we call sequence classes. Sequence classes cover diverse types of regulatory activities, such as promoter or cell type-specific enhancer activity, across the whole genome by integrating sequence-based predictions from histone marks, TFs and chromatin accessibility across a wide range of cell types. Importantly, sequence classes can be used to both classify and quantify the regulatory activities of any sequence based on predictions made by the deep learning sequence model, thereby allowing any mutation to be quantified by its impact (for example, increase, decrease or no change) on cell type-specific regulatory activities.

 

Thus, Sei enables an interpretable and systematic integration of sequence-based regulatory activity predictions with human genetics data to elucidate the regulatory basis of complex traits and diseases. We applied our framework to characterize disease- and trait-associated regulatory disruptions in GWAS data based on a nonoverlapping partitioning of heritability by regulatory activities. Moreover, we applied variant effect prediction at the sequence class-level to interpret cell type-specific regulatory mechanisms for individual disease mutations and differentiate between gain-of-function (GoF) and loss-of-function (LoF) regulatory mutations.

 

The Sei framework in its current form is provided as a resource for systematically classifying and scoring any sequence and variant with sequence classes, additionally providing the Sei model predictions for the 21,907 chromatin profiles underlying the sequence classes. The framework can be run using the code available at https://github.com/FunctionLab/sei-framework; a user-friendly web server is available at hb.flatironinstitute.org/sei.

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Europe's largest river, the river Rhine at risk of drying out as Europe suffers record drought due to global warming

Europe's largest river, the river Rhine at risk of drying out as Europe suffers record drought due to global warming | Amazing Science | Scoop.it
Lack of water has been a huge problem for Germany, with the continent’s misery deepening on news Wednesday that the Rhine river’s falling water levels could reach a critical level by the end of the week. A marker just west of Frankfurt was set to drop to just under 16 inches, meaning barges can’t carry vital transports of coal and diesel up the ancient river.

 

Germany's most-important river is running dry as Europe suffers through a drought that is on course to become its worst in 500 years, with terrifying wildfires burning once again in France.

Water levels in the Rhine - which carries 80 per cent of all goods transported by water in Germany, from its industrial heartlands to Dutch ports - are now so low that it could become impassable to barges later this week, threatening vital supplies of oil and coal that the country is relying upon as Russia turns off the gas tap.

The Rhine is already lower now than it was at the same point in 2018, when Europe suffered its last major drought. That year, the river ended up closing to goods vessels for 132 days, almost triggering a recession. Costs to transport goods by river this year have already risen five-fold as barges limit their capacity to stay afloat.

 

Economists estimate the disruption could knock as much as half a percentage point off Germany's overall economic growth this year, with experts warning the country was facing recession due to an energy crisis even before the drought hit. Andrea Toreti, senior researcher at the European Commission's Joint Research Centre, said: 'We haven't analysed fully [this] event, but based on my experience I think that this is perhaps even more extreme than in 2018.

 

'2018 was so extreme that looking back at this list of the last 500 years, there were no other events similar.' Meanwhile wildfires are once again ripping their way across France, torching an area that was already badly-hit as temperatures soared to record levels last month.

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AI Could Teach Smart Microrobots How to Swim and Maneuver

AI Could Teach Smart Microrobots How to Swim and Maneuver | Amazing Science | Scoop.it

Researchers from Santa Clara University, New Jersey Institute of Technology and the University of Hong Kong have been able to successfully teach microrobots how to swim via deep reinforcement learning, marking a substantial leap in the progression of microswimming capability.

 

There has been tremendous interest in developing artificial microswimmers that can navigate the world similarly to naturally-occurring swimming microorganisms, like bacteria. Such microswimmers provide promise for a vast array of future biomedical applications, such as targeted drug delivery and microsurgery. Yet, most artificial microswimmers to date can only perform relatively simple maneuvers with fixed locomotory gaits.

In the researchers' study published in Communications Physics, they reasoned microswimmers could learn -- and adapt to changing conditions -- through AI. Much like humans learning to swim require reinforcement learning and feedback to stay afloat and propel in various directions under changing conditions, so too must microswimmers, though with their unique set of challenges imposed by physics in the microscopic world.

 

"Being able to swim at the micro-scale by itself is a challenging task," said On Shun Pak, associate professor of mechanical engineering at Santa Clara University. "When you want a microswimmer to perform more sophisticated maneuvers, the design of their locomotory gaits can quickly become intractable."

 

By combining artificial neural networks with reinforcement learning, the team successfully taught a simple microswimmer to swim and navigate toward any arbitrary direction. When the swimmer moves in certain ways, it receives feedback on how good the particular action is. The swimmer then progressively learns how to swim based on its experiences interacting with the surrounding environment.

 

"Similar to a human learning how to swim, the microswimmer learns how to move its 'body parts' -- in this case three microparticles and extensible links -- to self-propel and turn," said Alan Tsang, assistant professor of mechanical engineering at the University of Hong Kong. "It does so without relying on human knowledge but only on a machine learning algorithm."

 

The AI-powered swimmer is able to switch between different locomotory gaits adaptively to navigate toward any target location on its own. As a demonstration of the powerful ability of the swimmer, the researchers showed that it could follow a complex path without being explicitly programmed. They also demonstrated the robust performance of the swimmer in navigating under the perturbations arising from external fluid flows.

 

"This is our first step in tackling the challenge of developing microswimmers that can adapt like biological cells in navigating complex environments autonomously," said Yuan-nan Young, professor of mathematical sciences at New Jersey Institute of Technology.

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Dwarf galaxies lack dark matter, new study suggests

Dwarf galaxies lack dark matter, new study suggests | Amazing Science | Scoop.it

Galaxies are thought to form inside immense halos of dark matter - an invisible form of matter that makes up most of the universe's mass. However, a new study suggests that dwarf galaxies of one of Earth's nearest clusters lack this dark matter.

 

According to the standard model of cosmology, the vast majority of galaxies are surrounded by a halo of dark matter particles. By showing that the dwarf galaxies - small, faint galaxies - of Earth's second closest galaxy cluster - named the Fornax Cluster - are free of such dark matter halos, the new study has challenged this view. The Fornax Cluster has a rich population of dwarf galaxies, with recent observations showing that some of these dwarfs appear distorted.

 

Dwarf galaxies can usually be found in galaxy clusters or near larger galaxies, because of which, they might be affected by the gravitational effects of their larger companions. Led by Elena Asencio, a PhD student at the University of Bonn, the study introduced an innovative way of testing the standard model based on how much dwarf galaxies are disturbed by gravitational tides from nearby larger galaxies.

 

"It was not expected that such perturbations should be present in the Fornax dwarfs. This is because, according to the standard model, the dark matter halos of these dwarfs should partly shield them from tides raised by the cluster," Pavel Kroupa, Professor at the University of Bonn and Charles University in Prague, said in a statement.

 

The researchers analyzed the expected level of disturbance of the dwarfs, which depends on their internal properties and their distance to the gravitationally powerful cluster centre and compared this with their observed level of disturbance evident from photographs. They found that if one wants to explain the observations in the standard model, the Fornax dwarfs should already be destroyed by gravity from the Fornax Cluster even when the tides it raises on a dwarf are 64 times weaker than the dwarf's own self-gravity.

 

The team concluded that the standard model cannot explain the observed morphologies of the Fornax dwarfs and the lack of fragile dwarfs towards its centre. They further repeated the analysis using Milgromian dynamics (MOND). Instead of assuming dark matter halos surrounding galaxies, MOND proposes a correction to Newtonian dynamics by which gravity experiences a boost in the regime of low accelerations.

 

"We were not sure that the dwarf galaxies would be able to survive the extreme environment of a galaxy cluster in MOND, due to the absence of protective dark matter halos in this model. But our results show a remarkable agreement between observations and the MOND expectations for the level of disturbance of the Fornax dwarfs," said Dr Indranil Banik of the School of Physics and Astronomy at St Andrews, who did much of the coding for this project.

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New York Polio Case Revives Questions about Live Oral Vaccine

New York Polio Case Revives Questions about Live Oral Vaccine | Amazing Science | Scoop.it

The first case of polio in the U.S. since 2013 was announced by New York state health officials on July 21, 2022. The U.S. resident had not yet been vaccinated. Polio was a common cause of paralysis in children before safe and effective vaccines were developed in the mid-20th century. Thanks to global vaccination campaigns, polio is now almost eradicated, with only 13 cases of endemic wild poliovirus reported in 2022 to date worldwide.  The New York patient reportedly contracted a form of polio that can be traced back to the live, but weakened, poliovirus used in the oral polio vaccine. This version of a vaccine has not been used in the U.S. since 2000. Health officials said the virus affecting the male patient, who has muscle weakness and paralysis, likely originated somewhere overseas, where oral vaccines are still administered. William Petri is an infectious disease specialist and chair of the World Health Organization’s Polio Research Committee. He explains what vaccine-derived poliovirus is and why the inactivated polio vaccine administered in the U.S. today can’t cause it. 

 

What are the two kinds of polio vaccine?

Vaccines introduce a harmless version of a pathogen to your body. The idea is that they train your immune system to fight off the real germ if you ever encounter it. The oral polio vaccine, originally developed by Albert Sabin, uses a live but weakened poliovirus that one swallows in a sugar cube or droplet. Scientists weaken – or attenuate – the virus so it can no longer cause disease.  The other kind of polio vaccine was originally developed by Jonas Salk. It contains inactivated, dead virus. It is administered by an injection. In the U.S., children receive the inactivated polio vaccine at 2, 4 and 6 months of age. It provides nearly complete protection from paralytic polio.

 

How can the live vaccine lead to a case of polio?

 

The weakened form of the live virus in the oral vaccine cannot cause disease. However, because the vaccine is given orally, the weakened virus is excreted in the feces and can spread from someone who is vaccinated to their close contacts. If the weakened virus circulates person to person for long enough, it can mutate and regain its ability to cause paralysis. The mutated virus can then infect people in communities with poor sanitation and low vaccination rates, causing disease and even paralysis.  This is an exceedingly rare occurrence. With more than 10 billion doses of the oral polio vaccine administered since 2000, there have been fewer than 800 cases of vaccine-derived polio reported. Apparently, the current patient in New York was somehow exposed to a mutated poliovirus that had been transmitted after vaccination overseas. Earlier this summer, routine surveillance spotted vaccine-derived poliovirus in London’s sewage system, but no cases have been reported there.

 

Why use the oral vaccine anywhere if it comes with this risk?

There’s a positive aspect to the fact that the weakened live virus can circulate in the community once oral vaccine recipients shed it in their feces. Traveling a feces-to-oral route, it can help induce immunity even in people who weren’t directly vaccinated. The oral polio vaccine is also cheaper and easier to administer than inactivated polio vaccines. Most importantly, the live-virus vaccine stops transmission of wild poliovirus in a way that the inactivated-virus vaccine does not. The eradication of polio in the Americas, Europe and Africa has been accomplished solely through the use of the live oral vaccine. Once polio has been wiped from a continent, then it is safe to stop using the oral live vaccine and use only the inactivated vaccine, which does prevent disease in recipients and does not pose the rare risk of vaccine-derived paralytic polio.  A new and safer oral polio vaccine that has been engineered not to mutate is now replacing the earlier live-virus vaccine. Thus, even this extremely rare complication of polio vaccination should soon become a thing of the past. 

 

How close is the world to eradicating polio?

Thanks to tremendous global effort, two of the three viruses that cause polio have been eradicated. The world is now on the verge of eradicating the final one, wild poliovirus 1 (WPV1). Today endemic polio is found only in Pakistan, with 12 cases of paralytic polio so far in 2022, and Afghanistan, with just one case this year. Africa has two cases, imported from overseas, which are being contained by additional vaccination campaigns. Once wild poliovirus has been eradicated from the planet, vaccination efforts may be able to switch to the inactivated polio vaccine, eliminating the risk of any future vaccine-derived cases.

 

This article was originally published on The Conversation. Read the original article.


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Alan D. Thompson's AI Roadmap (2022-2026): AI’s next big steps in the world (BCIs, Xiaomi CyberOne, Tesla Optimus, UBI, Sam Altman, etc.)

His website is here

 

Brain-machine interfaces are racing ahead. Just like the option of having a cell phone (mobile phone) or smart watch, you will have the option of connecting a brain-machine interface (BMI, also called a brain-computer interface, BCI). This is a wireless interface between your brain and the world, soon to be integrated with artificial intelligence. As of July 2022, people with ‘non-invasive’ Synchron brain implants (placed in a blood vessel) are already living among us. They are using their BMIs to shop online and chat on WhatsApp… using only thought. Push this out a few months, and you will be able to have instant cognitive access to whatever you need, whenever you need it.

 

Education is over. More accurately, education as we have known it is over. With an outdated, long-term, intergenerational view that we have to go to school, and then college, and then ‘make a living’ (whatever that means), it can be next to impossible to clear this old-fashioned understanding of the world from our collective minds. The number of colleges and universities—as well as overall enrolment—has been steadily collapsing over the last few years, accelerated by the 2019 pandemic. By default, we may assume that this is somehow ‘bad,’ but the ripple effects are wonderful.

 

Distributed income is next, and it is urgently necessary. There are many smart people working on many different forms of distributed income, usually called universal basic income (UBI). This is a mechanism where all citizens of a given population regularly receive a legally stipulated and equally set financial grant, without needing to give anything (like labor) in return.

 

Jobs are for robots, high unemployment is a good thing. Any change can seem jarring, but I definitely appreciate that this shift in perspective for a metric like unemployment is particularly discordant! For tens of thousands of years, humans have had jobs. From farming to executive coaching, we have found it necessary to swap the output of our minds and bodies for a tokenized representation of credits, which we can swap for things. This labor economy, and the entire branch of capitalism, has brought us to where we are today. Through artificial intelligence, the field of automation and robotics is quickly shifting us from a labor economy to a leisure economy. As robotics and artificial intelligence continue to outperform humans8 in several metrics, we will continue to see improvements in quality and efficiency across industries.

 

Mental wellness will be the new normal. How are your zinc and vitamin D levels today? These and many more markers change day-to-day and season-to-season, so a vitamin/hormone cocktail customized to your body and its responses brings an innovative metamorphosis for humanity. And there are even bigger applications of this tailored approach to ensuring that your biochemistry is optimized. Johns Hopkins University reports11 that 26% of adults in the US suffer from a diagnosable mental disorder in a given year. If that statistic were to be extended to the entire world population, we would have over 2 billion people with a diagnosable mental health issue in 2022.

 

The next step will be giant. You live in 2022. You have a front row seat to the most exciting period in human history. And perhaps most importantly, for some reason, you have unparalleled access to the inner workings of what’s going on. AI labs are extraordinarily and astonishingly open about their progress. You can read the AI papers at no charge, as they are released. You can play with many of the AI models, often for free. You are living in the future. And AI’s next big steps in the world are going to be groundbreaking.

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Genetically modified sterile mice produce rat sperm

Genetically modified sterile mice produce rat sperm | Amazing Science | Scoop.it

Researchers generated rat sperm cells inside sterile mice using a technique called blastocyst complementation.

 

"Our study shows that we can use sterile animals as hosts for the generation of germ cells from other animal species," says senior author Ori Bar-Nur, a stem cell biologist at ETH Zurich. "Aside from a conceptual advancement, this notion can be utilized to produce endangered animal species gametes inside more prevalent animals. Other implications may involve an improved method to produce rat transgenic models for biomedical research."

 

Pluripotent stem cells (PSCs) provide a powerful tool for biomedical research, but the generation of gametes in the form of eggs or sperm cells from PSCs is a highly challenging endeavor. In prior studies, researchers used a technique called blastocyst complementation to generate rat organs in mice using PSCs and mutated mouse embryos that cannot produce specific organs.

 

Building on this work, Bar-Nur and his collaborators wondered whether it would be possible to generate rat sperm inside mice that carry a genetic mutation that otherwise renders them sterile.

To test this idea, the researchers injected rat PSCs into mouse embryos to produce mouse-rat chimeras. An essential gene for sperm production was mutated in the mouse blastocysts. The rat stem cells developed together with the mouse cells, thereby generating a chimeric animal composed of genotypes from the two species. As a consequence of the genetic sterility-inducing mutation, an empty niche developed inside the testes, which enabled the rat cells to colonize them and exclusively generate rat sperm in mouse-rat chimeras. The sperm cells could fertilize rat egg cells, but the embryos did not develop normally or give rise to live offspring.

 

"We were surprised by the relative simplicity by which we could mix the two species to produce viable mouse-rat chimeras. These animals, by large, appeared healthy and developed normally, although they carried both mouse and rat cells in a chimeric animal," Bar-Nur says. "The second surprise was that indeed all the sperm cells inside the chimeras were of rat origin. As such, the mouse host environment, which was sterile due to a genetic mutation, was still able to support efficient sperm cell production from a different animal species."

 

Although the researchers were able to generate rat sperm cells that morphologically appeared indistinguishable from normal rat sperm cells, these cells were immotile and the fertilization rates of rat eggs was significantly lower in comparison to rat sperm cells produced in rats. Nonetheless, the work provides a proof-of-principle that one can generate sperm cells of one animal species in another by mixing the two species in an artificially generated organism called a chimera. Using sterile mice for genetically modified rat PSCs may speed up the production of transgenic rats to model human diseases in biomedical research.

 

Moving forward, the researchers will try to produce live animals from rat sperm cells that have been produced in mouse-rat chimeras. "We will need to improve the technique and demonstrate that rat sperm produced in mice can give rise to adult rats when fertilizing rat eggs," Bar-Nur says.

 

A more distant plan is to adapt this technique for the production of gametes from endangered rodent species to support animal species conservation efforts. "For example, to the extent we can procure stem cells from an endangered rodent, which at some point in time might become extinct, we may be able to employ the same method to produce its germ cells via chimera production with mice," Bar-Nur says. "However, it is important to note that several scientific hurdles will need to be overcome to adapt this technique to other animal species. In addition, one still needs to showcase the production of female reproductive cells (i.e., eggs) in female sterile mice, especially if we envision utilizing this technology for species conservation efforts."

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A simple way of sculpting matter into complex shapes

A simple way of sculpting matter into complex shapes | Amazing Science | Scoop.it
A new method for shaping matter into complex shapes, with the use of 'twisted' light, has been demonstrated in research at the University of Strathclyde.

 

When atoms are cooled to temperatures close to absolute zero (-273 degrees C), they stop behaving like particles and start to behave like waves. Atoms in this condition, which are known as Bose–Einstein condensates (BECs), are useful for purposes such as realization of atom lasers, slow light, quantum simulations for understanding the complex behavior of materials like superconductors and superfluids, and the precision measurement technique of atom interferometry.

 

The Strathclyde study has shown that when twisted light is shone on to a moving BEC, it breaks into clusters of BEC droplets that move following the light's features, with the number of droplets equal to twice the number of light twists. Altering the properties of the light beam can change both the number of BEC droplets and the way that they move.

 

The research has been published in Physical Review Letters.

Grant Henderson, a Ph.D. student in Strathclyde's Department of Physics, is lead author on the paper. He said: "By shining a laser beam on to a BEC, we can influence how it behaves. When the laser beam is "twisted," it has a helical phase profile and carries orbital angular momentum (OAM). Laser beams with OAM can trap and rotate microscopic particles, behaving like an optical spanner.

 

"This method of shining twisted light through ultracold atoms opens a new and simple way of sculpting matter into unconventional and complex shapes. It has the potential for the design of novel quantum devices such as atomtronic circuits and ultra-sensitive detectors."

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High aerodynamic lift from the tail reduces drag in gliding birds

High aerodynamic lift from the tail reduces drag in gliding birds | Amazing Science | Scoop.it

Many functions have been postulated for the aerodynamic role of the avian tail during steady-state flight. By analogy with conventional aircraft, the tail might provide passive pitch stability if it produced very low or negative lift. Alternatively, aeronautical principles might suggest strategies that allow the tail to reduce inviscid, induced drag: if the wings and tail act in different horizontal planes, they might benefit from biplane-like aerodynamics; if they act in the same plane, lift from the tail might compensate for lift lost over the fuselage (body), reducing induced drag with a more even downwash profile. However, textbook aeronautical principles should be applied with caution because birds have highly capable sensing and active control, presumably reducing the demand for passive aerodynamic stability, and, because of their small size and low flight speeds, operate at Reynolds numbers two orders of magnitude below those of light aircraft.

 

An owl bursting through a cloud of bubbles is helping researchers better understand the aerodynamics of flight. Researchers in London have discovered a new way in which birds use their tail to provide lift and so reduce drag while gliding. They tracked the swirling motion of more than 20,000 helium-filled soap bubbles as they were displaced by birds of prey in flight. Their findings could provide a new way to improve the efficiency of small gliding aircraft.

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The geometry of life: when mathematics meets synthetic biology

The geometry of life: when mathematics meets synthetic biology | Amazing Science | Scoop.it

Youtube video is here

 

Tiling patterns can be found thoughout the natural world - from honeycomb to fish scales. But now researchers have come up with a new way to create patterns in petri dishes using bacteria. By engineering bacterial cells to express uniquely adhesive proteins on their surface, the team could create linear patterns - formed as colonies of cells stuck together when they grew. What's more, by varying the exact proteins expressed and modeling where to place the bacterial cells, they were able to control the resulting geometry - creating a range of complex patterns.


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Langya henipavirus virus outbreak: How worrying is the new animal-to-human LayV virus from China?

Langya henipavirus virus outbreak: How worrying is the new animal-to-human LayV virus from China? | Amazing Science | Scoop.it

While the threat of COVID-19 still lingers two years on from the start of the pandemic and the outbreak of monkeypox is far from being contained, a new virus is looming over the horizon. Again coming from China. Researchers are monitoring the spread of the novel Langya henipavirus (LayV) in China, where dozens of cases have already been reported. The virus was first detected in 2018 in the northeastern provinces of Shandong and Henan but was only officially identified last week after China experienced a sudden surge in cases, now up to a total of 35.

 

According to a new study by ​​the Beijing Institute of Microbiology and Epidemiology published last week, the Langya virus cases were identified after several patients experiencing a fever and reporting a history of animal exposure in eastern China were examined by health officials as part of a health surveillance project. After identifying the Langya virus in one of the patient’s throat swabs, the researchers found the presence of the virus in 35 people - mostly farmers - in the Shandong and Henan provinces.

 
What is the Langya virus?

The Langya virus belongs to the same family as the deadly Nipah and Hendra viruses, the henipavirus family. According to the World Health Organization (WHO), this family of viruses is highly dangerous, with Nipah being estimated to have a fatality rate between 40 to 75 per cent - much higher than the death rate reported for COVID-19. It’s unclear how dangerous the Langya virus could be to humanity, as all the patients who contracted the virus in China so far experienced mild flu-like symptoms, and there were no related fatalities reported.

 

The henipavirus viruses are naturally harboured by pteropid fruit bats (flying foxes) and microbats of several species, according to a Chinese study from 2008, but other studies have found other henipaviruses in bats, rodents, and shrews.

 

What are its symptoms of Langya virus?

The most common symptom of the Langya virus appears to be a fever (experienced by all patients), but those infected with the virus also reported fatigue (54 per cent of patients), loss of appetite (50 per cent), muscle pain (46 per cent), cough (50 per cent), nausea (38 per cent), headache and vomiting (35 per cent) after contracting the virus. Several also developed blood cell abnormalities and signs of liver and kidney damage, but none of the infected patients died.

 

How does Langya virus get transmitted?

The Langya virus is a zoonotic infection - meaning the virus is spread from animals to humans. But as none of the patients in China had close contact with each other, experts believe that the transmission of the virus from animal to human is still sporadic. Researchers in China are still trying to find exactly what animals were involved in the virus transmission, but they suspect shrews might be involved.

 

Scientists at the Beijing Institute of Microbiology and Epidemiology found that among 25 species of wild small animals surveyed, the genome of the virus was predominantly detected in shrews, with 27 per cent of 262 shrews examined found to be harbouring the virus. This could potentially mean that the tiny animal may be a natural reservoir of the Langya virus.

 

While it’s certain that the virus was transmitted from an animal to a human, researchers are still unsure about whether human-to-human transmission is possible at all. According to the Chinese scientists, contact tracing of 9 patients with 15 close-contact family members revealed no transmission of the virus. But the same researchers believe the sample analysed is too small to determine whether human-to-human transmission is possible.

 

Is there a vaccine or treatment?

There are currently no vaccines for humans for henipaviruses, though one against Hendra virus exists for horses. No effective anti-viral treatment is known either other than treating the symptoms.

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Improving Image Sensors for Machine Vision

Improving Image Sensors for Machine Vision | Amazing Science | Scoop.it

 Image sensors measure light intensity, but angle, spectrum, and other aspects of light must also be extracted to significantly advance machine vision. In Applied Physics Letters, published by AIP Publishing, researchers at the University of Wisconsin-Madison, Washington University in St. Louis, and OmniVision Technologies highlight the latest nano-structured components integrated on image sensor chips that are most likely to make the biggest impact in multimodal imaging. The developments could enable autonomous vehicles to see around corners instead of just a straight line, biomedical imaging to detect abnormalities at different tissue depths, and telescopes to see through interstellar dust.

 

“Image sensors will gradually undergo a transition to become the ideal artificial eyes of machines,” co-author Yurui Qu, from the University of Wisconsin-Madison, said. “An evolution leveraging the remarkable achievement of existing imaging sensors is likely to generate more immediate impacts.” Image sensors, which converts light into electrical signals, are composed of millions of pixels on a single chip. The challenge is how to combine and miniaturize multifunctional components as part of the sensor.

 

In their own work, the researchers detailed a promising approach to detect multiple-band spectra by fabricating an on-chip spectrometer. They deposited photonic crystal filters made up of silicon directly on top of the pixels to create complex interactions between incident light and the sensor. The pixels beneath the films record the distribution of light energy, from which light spectral information can be inferred. The device – less than a hundredth of a square inch in size – is programmable to meet various dynamic ranges, resolution levels, and almost any spectral regime from visible to infrared.

 

The researchers built a component that detects angular information to measure depth and construct 3D shapes at subcellular scales. Their work was inspired by directional hearing sensors found in animals, like geckos, whose heads are too small to determine where sound is coming from in the same way humans and other animals can. Instead, they use coupled eardrums to measure the direction of sound within a size that is orders of magnitude smaller than the corresponding acoustic wavelength.

 

Similarly, pairs of silicon nanowires were constructed as resonators to support optical resonance. The optical energy stored in two resonators is sensitive to the incident angle. The wire closest to the light sends the strongest current. By comparing the strongest and weakest currents from both wires, the angle of the incoming light waves can be determined. Millions of these nanowires can be placed on a 1-square-millimeter chip. The research could support advances in lensless cameras, augmented reality, and robotic vision.

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New quantum whirlpools with tetrahedral symmetries discovered in a superfluid

New quantum whirlpools with tetrahedral symmetries discovered in a superfluid | Amazing Science | Scoop.it

An international collaboration of scientists has created and observed an entirely new class of vortices -- the whirling masses of fluid or air. Led by researchers from Amherst College in the US and the University of East Anglia and Lancaster University in the UK, their new paper details the first laboratory studies of these 'exotic' whirlpools in an ultracold gas of atoms at temperatures as low as tens of billionths of a degree above absolute zero.

 

The discovery, announced this week in the journal Nature Communications, may have exciting future implications for implementations of quantum information and computing.

Vortices are familiar objects in nature, from the whirlpools of water down a bathtub drain to the airflow around a hurricane.

 

In quantum-mechanical systems, such as an atomic Bose-Einstein condensate, the vortices tend to be tiny and their circulation comes in discrete, quantized units. Such vortices have long been objects of fascination for physicists and have helped to illuminate the unusual properties of superfluidity and superconductivity. The unusual nature of the observed whirlpools here, however, is due to symmetries in the quantum gas. One especially fascinating property of physical theories, from cosmology to elementary particles, is the appearance of asymmetric worlds despite perfect underlying symmetries. For example, when water freezes to ice, disordered molecules in a liquid arrange themselves into a periodic array.

 

The spatial symmetry of a system is often readily identified -- for example, a honeycomb has a periodic array of cells with hexagonal symmetry. Although the vortex medium used in this new work is a fluid rather than a solid array, it also possesses an internal set of hidden discrete symmetries. For example, one of the team's ultracold gases had the fourfold symmetry of a square, and another had the tetrahedral symmetry of a four-sided die, familiar to players of fantasy games everywhere. "The mass flow and the underlying symmetry of the fluid interact with one another in interesting ways," said Dr Magnus Borgh, Associate Professor in Physics at UEA.

 

"One consequence is that if the positions of two vortices are interchanged, they can leave a trace of the process lingering in the fluid. This trace links the interacting vortices together permanently, like a rung in a ladder. No ordinary fluids behave like this, and it may be that analogous objects only exist deep inside neutron stars," added Prof Janne Ruostekoski, of Lancaster University. Indeed, the team says these created vortices go beyond the state-of-the-art.

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NASA: Kepler Catches the Earliest Flash of a Supernova

NASA: Kepler Catches the Earliest Flash of a Supernova | Amazing Science | Scoop.it

The brilliant flash of an exploding star’s shockwave—what astronomers call the “shock breakout”—has been captured for the first time in the optical wavelength or visible light by NASA's planet-hunter, the Kepler space telescope.

 

An international science team led by Peter Garnavich, an astrophysics professor at the University of Notre Dame in Indiana, analyzed light captured by Kepler every 30 minutes over a three-year period from 500 distant galaxies, searching some 50 trillion stars. They were hunting for signs of massive stellar death explosions known as supernovae.

 

The above diagram illustrates the brightness of a supernova event relative to the sun as it unfolds. For the first time, a supernova shockwave has been observed in the visible light window as it reaches the surface of the star. This early flash of light is called a shock breakout. The explosive death of this doomed star, called KSN2911d, as it reaches its maximum brightness takes about 14 days in total. The shock breakout itself lasts just about 20 minutes, so catching the flash of energy is an investigative milestone for astronomer. The unceasing gaze of NASA's Kepler space telescope allowed astronomers to see, at last, this early moment as the star blows up. Supernovae like these - known as Type II - begin when the internal furnace of a star runs out of nuclear fuel causing its core to collapse as the gravity takes over. This type of star is called a red supergiant and it is 20,000 times brighter than our sun. As the supergiant star goes supernova, the energy traveling from the core reaches the surface with a burst of light that is 130,000,000 times brighter than the sun. The star continues to explode and grow in size reaching a maximum brightness that is about 1 Billion times brighter than the sun.

 

In 2011, two of these massive stars, called red supergiants, exploded while in Kepler’s view. The first behemoth, KSN 2011a, is nearly 300 times the size of our sun and a mere 700 million light years from Earth. The second, KSN 2011d, is roughly 500 times the size of our sun and around 1.2 billion light years away.“To put their size into perspective, Earth's orbit about our sun would fit comfortably within these colossal stars,” said Garnavich.

 

Whether it’s a plane crash, car wreck or supernova, capturing images of sudden, catastrophic events is extremely difficult but tremendously helpful in understanding root cause. Just as widespread deployment of mobile cameras has made forensic videos more common, the steady gaze of Kepler allowed astronomers to see, at last, a supernova shockwave as it reached the surface of a star. The shock breakout itself lasts only about 20 minutes, so catching the flash of energy is an investigative milestone for astronomers.

 

“In order to see something that happens on timescales of minutes, like a shock breakout, you want to have a camera continuously monitoring the sky,” said Garnavich. “You don’t know when a supernova is going to go off, and Kepler's vigilance allowed us to be a witness as the explosion began.” The two supernovae matched up well with mathematical models of Type II explosions reinforcing existing theories. But they also revealed what could turn out to be an unexpected variety in the individual details of these cataclysmic stellar events.

 

While both explosions delivered a similar energetic punch, no shock breakout was seen in the smaller of the supergiants. Scientists think that is likely due to the smaller star being surrounded by gas, perhaps enough to mask the shockwave when it reached the star's surface.

 

“That is the puzzle of these results,” said Garnavich. “You look at two supernovae and see two different things. That’s maximum diversity.” Understanding the physics of these violent events allows scientists to better understand how the seeds of chemical complexity and life itself have been scattered in space and time in our Milky Way galaxy

 

"All heavy elements in the universe come from supernova explosions. For example, all the silver, nickel, and copper in the earth and even in our bodies came from the explosive death throes of stars," said Steve Howell, project scientist for NASA's Kepler and K2 missions at NASA’s Ames Research Center in California's Silicon Valley. "Life exists because of supernovae."

 

Garnavich is part of a research team known as the Kepler Extragalactic Survey or KEGS. The team is nearly finished mining data from Kepler’s primary mission, which ended in 2013 with the failure of reaction wheels that helped keep the spacecraft steady. However, with the reboot of the Kepler spacecraft as NASA's K2 mission, the team is now combing through more data hunting for supernova events in even more galaxies far, far away.

 

"While Kepler cracked the door open on observing the development of these spectacular events, K2 will push it wide open observing dozens more supernovae," said Tom Barclay, senior research scientist and director of the Kepler and K2 guest observer office at Ames. "These results are a tantalizing preamble to what's to come from K2!"

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Without any prior knowledge AI program uncovered novel relevant variables from performing experiments

Without any prior knowledge AI program uncovered novel relevant variables from performing experiments | Amazing Science | Scoop.it

A new AI program observed physical phenomena and uncovered relevant variables—a necessary precursor to any physics theory.

 

All physical laws are described as mathematical relationships between state variables. These variables give a complete and non-redundant description of the relevant system. However, despite the prevalence of computing power and artificial intelligence, the process of identifying the hidden state variables themselves has resisted automation. Most data-driven methods for modeling physical phenomena still rely on the assumption that the relevant state variables are already known. A longstanding question is whether it is possible to identify state variables from only high-dimensional observational data.

 

Scientists now created a principle for determining how many state variables an observed system is likely to have, and what these variables might be. They were able to demonstrate the effectiveness of this approach using video recordings of a variety of physical dynamical systems, ranging from elastic double pendulums to fire flames. Without any prior knowledge of the underlying physics, our algorithm discovers the intrinsic dimension of the observed dynamics and identifies candidate sets of state variables.

 

Github repository is here

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Super-Earth Found in Habitable Zone of Red Dwarf

Super-Earth Found in Habitable Zone of Red Dwarf | Amazing Science | Scoop.it
A super-Earth planet has been found near the habitable zone of a red dwarf star only 37 light-years from the Earth. This is the first discovery by a new instrument on the Subaru Telescope and offers a chance to investigate the possibility of life on planets around nearby stars. With such a successful first result, we can expect that the Subaru Telescope will discover more, potentially even better, candidates for habitable planets around red dwarfs.

 

Red dwarfs, stars smaller than the Sun, account for three-quarters of the stars in the Milky Way Galaxy, and are abundant in the neighborhood around the Sun. As such, they are important targets in the search for nearby extra-solar planets and extraterrestrial life. But red dwarfs are cool and don't emit much visible light compared to other types of stars, making it difficult to study them.

 

In the infrared wavelengths red dwarfs are brighter. So the Astrobiology Center in Japan developed an infrared observational instrument mounted on the Subaru Telescope to search for signs of planets around red dwarf stars. The instrument is called IRD for Infrared Doppler, the observational method used in this search.

 

The first fruits of this search are signs of a super-Earth four times the mass of the Earth circling the star Ross 508, located 37 light-years away in the constellation Serpens. This planet, Ross 508 b, has a year of only 11 Earth-days, and lies at the inner edge of the habitable zone around its host star. Interestingly, there are indications that the orbit is elliptical, which would mean that for part of the orbit the planet would be in the habitable zone, the region where conditions would be right for liquid water to exist on the surface of the planet. Whether or not there is actually water or life are questions of further study.

 

To have the very first planet discovered by this new method be so tantalizingly close to the habitable zone seems too good to be true and bodes well for future discoveries. Bun'ei Sato, a Professor at the Tokyo Institute of Technology and the principal investigator in this search comments, "It has been 14 years since the start of IRD's development. We have continued our development and research with the hope of finding a planet exactly like Ross 508 b."

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Mystery Objects in the Universe: 55 Years of Pulsar Science

This year marks the 55th anniversary of the discovery of pulsars, made by Dame Prof. Jocelyn Bell Burnell. Since then, we’ve learned so much about these intriguing objects, whilst they’ve taught us so much about the Galaxy too.

 

The first exoplanets ever discovered, 30 years ago this year, were also found around a pulsar. Once again the highly accurate nature of observing the periodic ticking of pulsars allowed astronomers to calculate the delay in the signal arrival time, finding that it matched the exact pattern that would be expected if there were not one, but two, small planets that were slightly tugging on the pulsar.

 

Pulsars have also given us a chance to learn about all the stuff between us and the stars in our Milky Way Galaxy thanks to their radio beams of light they emit. As this light travels across the interstellar medium (ISM), an inhomogeneous, turbulent mixture of ionized, atomic and molecular gas (as well as some dust), the pulsar’s signal is affected. For example, as the pulsar signal encounters the magnetic fields of the ISM, its polarization orientation can experience changes as it encounters a variety of magnetic fields along its path, and by the time it gets to Earth - these measured changes can tell us about the magnetic field of the entire Galaxy. 

 

Since their discovery by Bell Burnell, pulsar science has taken off - and Australian astronomers have been contributing to this field for decades. In fact, most pulsars we know about have been found using the Parkes radio telescope, owned and operated by Australia’s national science agency, CSIRO. But along with discovery and decades of science papers - we’ve captured some pulsar science stories from our local astronomy communities, that has added global value. 

PULSARS ARE STRANGE OBJECTS

One of the most powerful properties of pulsars is their regular, clock-like ticking, due to its consistency. But when astronomers first started observing these ticks, they noticed that for every revolution the star makes, the period would increase by an extraordinarily small amount. This gave us another tool to use - if we knew exactly how much the period was increasing, then we could predict how fast the pulsar would be spinning in a day, year or decade from now. And so, astronomers devised experiments around this - to keep monitoring pulsars to see if they followed the predicted models. But they didn’t. 

 

Every now and then, some pulsars would momentarily speed up, in small but measurable little jolts. This effect is known as glitching and helps astronomers to figure out what is going on, in the interior of these dense objects. One pulsar stunned astronomers when it glitched for the first time after 30 years of observations. 

 

Along with radio waves, pulsars also emit in other parts of the electromagnetic spectrum - especially in the higher energy bands, such as gamma rays and X-rays. Space-based observatories (that look at the light in these bands) have found many pulsars that are bright and emitting across the Galaxy in these energy regimes. An interesting mystery that is currently being investigated is that there appears to be an excess of gamma rays emanating from the Milky Way’s Galactic centre. A number of models have been put forward to explain this, including the possibility of dark matter annihilating in this region, or the more favorable idea that this excess of high energy is coming from millisecond pulsars. 

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Speeding up evolution at the genome level by alternative chromosome configuration

Speeding up evolution at the genome level by alternative chromosome configuration | Amazing Science | Scoop.it

A research team led by André Marques at the Max Planck Institute for Plant Breeding Research in Cologne, Germany, has uncovered the profound effects of an atypical mode of chromosome arrangement on genome organization and evolution. Their findings are published in the journal Cell.

 

In each individual cell in our body, our DNA, the molecule carrying the instructions for development and growth, is packaged together with proteins into structures called chromosomes. Full sets of chromosomes together constitute the genome, the entire genetic information of an organism. In most organisms, including us, chromosomes appear as X-shaped structures when they are captured in their condensed, duplicated states in preparation for cell division. Indeed, these structures may be among the most iconic in all of science. The X shape is due to a constricted region called the centromere that serves to connect sister chromatids, which are the identical copies formed by the DNA replication of a chromosome.

 

Most studied organisms are 'monocentric', meaning that centromeres are restricted to a single region on each chromosome. Several animal and plant organisms, however, show a very different centromere organization: instead of one solitary constriction as in the classic X-shaped chromosomes, chromosomes in these organisms harbor multiple centromeres that are arranged in a line from one end of a sister chromatid to the other. Thus, these chromosomes lack a primary constriction and the X shape, and species with such chromosomes are known as 'holocentric', from the ancient Greek word hólos meaning 'whole'.

 

A new study led by André Marques from the Max Planck Institute for Plant Breeding Research in Cologne, Germany, now reveals the striking effects of this non-classical mode of chromosome organization on genome architecture and evolution. To determine how holocentricity affects the genome, Marques and his team used highly accurate DNA sequencing technology to decode the genomes of three closely related holocentric beak-sedges, grass-like flowering plants found worldwide that are often the first conquerors of new habitats. For reference, the team also decoded the genome of their most closely related monocentric relative. Thus, comparing the holocentric beak-sedges with their monocentric relative allowed the authors to attribute any differences they observed to the effects of holocentricity.

 

Their analysis reveals striking differences in genome organization and chromosome behavior in holocentric organisms. They found that centromere function is distributed across hundreds of small centromere domains in holocentric chromosomes. While in monocentric organisms, genes are largely concentrated distant from centromeres and the regions immediately around them, in holocentric species they are uniformly distributed over the whole length of chromosomes. Further, in monocentric species chromosomes are known to engage in a high degree of intermingling with each other during cell division, a property which appears to play a role in regulating gene expression. Notably, these long-range interactions were sharply diminished in the beak-sedges with holocentromeres. Thus, holocentricity fundamentally affects genome organization as well as how chromosomes behave during cell division.

 

In holocentric organisms, almost any given chromosomal fragment will harbor a centromere and will thus have proper centromere function, which is not true for monocentric species. In this way, holocentromeres have been thought to stabilize chromosomal fragments and fusions and thus promote rapid genome evolution, or the ability of an organism to make prompt, wholesale changes to its DNA. In one of the beak-sedges they analyzed, Marques and his team could show that chromosome fusions facilitated by holocentromeres allowed this species to maintain the same chromosome number even after quadruplication of the entire genome. In another of their analyzed beak-sedges, a species with only two chromosomes, the lowest of any plant, holocentricity was found to be responsible for the dramatic reduction in chromosome number. Thus, holocentric chromosomes may allow the formation of news species through rapid evolution at genome-level.

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