Artificial Intelligence Edges Closer to the Clinic

TransMED can help predict the outcomes of COVID-19 patients, generating predictions from different kinds of clinical data, including clinical notes, laboratory tests, diagnosis codes and prescribed drugs. The other uniqueness of TransMED lies in its ability to transfer learn from existing diseases to better predict and reason about progression of new and rare diseases. 
Credit: Shannon Colson | Pacific Northwest National Laboratory

The beginning of the COVID-19 pandemic presented a huge challenge to healthcare workers. Doctors struggled to predict how different patients would fare under treatment against the novel SARS-CoV-2 virus. Deciding how to triage medical resources when presented with very little information took a mental and physical toll on caregivers as the pandemic progressed.

To ease this burden, researchers at Pacific Northwest National Laboratory (PNNL), Stanford University, Virginia Tech, and John Snow Labs developed TransMED, a first-of-its-kind artificial intelligence (AI) prediction tool aimed at addressing issues caused by emerging or rare diseases.

“As COVID-19 unfolded over 2020, it brought a number of us together into thinking how and where we could contribute meaningfully,” said chief scientist Sutanay Choudhury. “We decided we could make the most impact if we worked on the problem of predicting patient outcomes.”

“COVID presented a unique challenge,” said Khushbu Agarwal, lead author of the study published in Nature Scientific Reports. “We had very limited patient data for training an AI model that could learn the complex patterns underlying COVID patient trajectories.”

The multi-institutional team developed TransMED to address this challenge, analyzing data from existing diseases to predict outcomes of an emerging disease.

New Method to Promote Biofilm Formation and Increase Efficiency of Biocatalysis

 The researchers screened synthetic polymers for their ability to induce biofilm formation in a strain of E. coli (MC4100), which is known to be poor at forming biofilms. They also monitored the biomass and biocatalytic activity of both MC4100 and PHL644 (a good biofilm former), incubated the presence of these polymers, and found that MC4100 matched and even outperformed PHL644.
Credit: EzumeImages

Birmingham scientists have revealed a new method to increase efficiency in biocatalysis, in a paper published today in Materials Horizons.

Biocatalysis uses enzymes, cells or microbes to catalyze chemical reactions, and is used in settings such as the food and chemical industries to make products that are not accessible by chemical synthesis. It can produce pharmaceuticals, fine chemicals, or food ingredients on an industrial scale.

However, a major challenge in biocatalysis is that the most commonly used microbes, such as probiotics and non-pathogenic strains of Escherichia coli, are not necessarily good at forming biofilms, the growth promoting ecosystems that form a protective micro-environment around communities of microbes and increase their resilience and so boost productivity.

This problem is normally solved by genetic engineering, but researchers Dr Tim Overton from the university’s School of Chemical Engineering, and Dr Francisco Fernández Trillo from the School of Chemistry*, both of whom are members of the Institute of Microbiology and Infection, set out to create an alternative method to bypass this costly and time-consuming process.

The researchers identified a library of synthetic polymers and screened them for their ability to induce biofilm formation in E. coli, a bacterium that is one of the most widely studied micro-organisms, and commonly used in biocatalysis.

Why are some birds more intelligent than others?

Barbados bullfinch flying off with sugar packet.
Resized Image using AI by SFLORG
Source: McGill University

If you’ve ever seen a starling peck open a garbage bag or a grackle steal your dog pellets, you get a sense that some birds have learned to take advantage of new feeding opportunities – a clear sign of their intelligence. Scientists have long wondered why certain species of birds are more innovative than others, and whether these capacities stem from larger brains (which intuitively seems likely) or from a greater number of neurons in specific areas of the brain.

It turns out that it’s a bit of both, according to a recent study by an international team that included members from McGill University published in Nature Ecology and Evolution.

More neurons in the right place tied to greater intelligence in birds

The researchers used a new technique to estimate the number of neurons in a specific part of the brain called the pallium in 111 bird species. The pallium in birds is the equivalent of the human cerebral cortex, which is involved in memory, learning, reasoning, and problem-solving, among other things. When these estimates about neuron numbers in the pallium were combined with information about over 4,000 foraging innovations, the team found that the species with the higher numbers of neurons in the pallium were also likely to be the most innovative.

Scientists reveal distribution of dark matter around galaxies 12 billion years ago–further back in time than ever before

 The radiation residue from the Big Bang, distorted by dark matter 12 billion years ago.
Credit: Reiko Matsushita

A collaboration led by scientists at Nagoya University in Japan has investigated the nature of dark matter surrounding galaxies seen as they were 12 billion years ago, billions of years further back in time than ever before. Their findings, published in Physical Review Letters, offer the tantalizing possibility that the fundamental rules of cosmology may differ when examining the early history of our universe.

Seeing something that happened such a long time ago is difficult. Because of the finite speed of light, we see distant galaxies not as they are today, but as they were billions of years ago. But even more challenging is observing dark matter, which does not emit light.

Consider a distant source galaxy, even further away than the galaxy whose dark matter one wants to investigate. The gravitational pull of the foreground galaxy, including its dark matter, distorts the surrounding space and time, as predicted by Einstein’s theory of general relativity. As the light from the source galaxy travels through this distortion, it bends, changing the apparent shape of the galaxy. The greater the amount of dark matter, the greater the distortion. Thus, scientists can measure the amount of dark matter around the foreground galaxy (the “lens” galaxy) from the distortion.

However, beyond a certain point scientists encounter a problem. The galaxies in the deepest reaches of the universe are incredibly faint. As a result, the further away from Earth we look, the less effective this technique becomes. The lensing distortion is subtle and difficult to detect in most cases, so many background galaxies are necessary to detect the signal.

New Mexico Mammoths Among Best Evidence for Early Humans in North America

Close up of the bone pile during excavation. This random mix of ribs, broken cranial bones, a molar, bone fragments, and stone cobbles is a refuse pile from the butchered mammoths. It was preserved beneath the adult mammoth’s skull and tusks.
Credit: Timothy Rowe / The University of Texas at Austin.

About 37,000 years ago, a mother mammoth and her calf met their end at the hands of human beings.

Bones from the butchering site record how humans shaped pieces of their long bones into disposable blades to break down their carcasses, and rendered their fat over a fire. But a key detail sets this site apart from others from this era. It’s in New Mexico – a place where most archaeological evidence does not place humans until tens of thousands of years later.

A recent study led by scientists with The University of Texas at Austin finds that the site offers some of the most conclusive evidence for humans settling in North America much earlier than conventionally thought.

The researchers revealed a wealth of evidence rarely found in one place. It includes fossils with blunt-force fractures, bone flake knives with worn edges, and signs of controlled fire. And thanks to carbon dating analysis on collagen extracted from the mammoth bones, the site also comes with a settled age of 36,250 to 38,900 years old, making it among the oldest known sites left behind by ancient humans in North America.

“What we’ve got is amazing,” said lead author Timothy Rowe, a paleontologist and a professor in the UT Jackson School of Geosciences. “It’s not a charismatic site with a beautiful skeleton laid out on its side. It’s all busted up. But that’s what the story is.”

NIST Researchers Develop Miniature Lens for Trapping Atoms

Graphical illustration of light focusing using a planar glass surface studded with millions of nanopillars (referred to as a metalens) forming an optical tweezer. (A) Device cross section depicts plane waves of light that come to a focus through secondary wavelets generated by nanopillars of varying size. (B) The same metalens is used to trap and image single rubidium atoms.
Credit: Sean Kelley/NIST

Atoms are notoriously difficult to control. They zigzag like fireflies, tunnel out of the strongest containers and jitter even at temperatures near absolute zero.

Nonetheless, scientists need to trap and manipulate single atoms in order for quantum devices, such as atomic clocks or quantum computers, to operate properly. If individual atoms can be corralled and controlled in large arrays, they can serve as quantum bits, or qubits — tiny discrete units of information whose state or orientation may eventually be used to carry out calculations at speeds far greater than the fastest supercomputer.

Researchers at the National Institute of Standards and Technology (NIST), together with collaborators from JILA — a joint institute of the University of Colorado and NIST in Boulder — have for the first time demonstrated that they can trap single atoms using a novel miniaturized version of “optical tweezers” — a system that grabs atoms using a laser beam as chopsticks.

Ordinarily, optical tweezers, which garnered the 2018 Nobel Prize in Physics, feature bulky centimeter-size lenses or microscope objectives outside the vacuum holding individual atoms. NIST and JILA have previously used the technique with great success to create an atomic clock.

In the new design, instead of typical lenses, the NIST team used unconventional optics — a square glass wafer about 4 millimeters in length imprinted with millions of pillars only a few hundreds of nanometers (billionths of a meter) in height that collectively act as tiny lenses. These imprinted surfaces, dubbed metasurfaces, focus laser light to trap, manipulate and image individual atoms within a vapor. The metasurfaces can operate in the vacuum where the cloud of trapped atoms is located, unlike ordinary optical tweezers.

Triazavirin to Be Tested for Effectiveness Against Tick-Borne Encephalitis

Triazavirin was developed by scientists of the Ural Federal University and the Ural Branch of the Russian Academy of Sciences.
Credit: UrFU Press Service

The scientific community has provided research recommendations

The Medsintez plant, the manufacturer of the antiviral drug Triazavirin, plans to conduct studies of the drug for effectiveness against tick-borne encephalitis. Aleksandr Petrov, Chairman of the Board of Directors of the Medsintez Plant LLC, notes that the company has already received recommendations from the scientific community. This was reported by TASS.

"The effectiveness of Triazavirin against tick-borne encephalitis is a very interesting topic to study. Scientists are already saying that the drug can be effective against this virus. Currently we are guided by the opinion of scientists, that is why we are considering the possibility of conducting such studies," said Petrov.

He stressed that this year in some regions there is a high activity of ticks and increased detection of cases of encephalitis, that is why Triazavirin research in this area is relevant.

Reference:
Medsintez plant is located in Novouralsk (Sverdlovsk region). It specializes in the production of pharmaceutical products. The plant produces infusion solutions, ready forms of genetically engineered human insulin, solid and liquid forms of drugs. The plant manufactures licensed products and is engaged in the creation of new drugs.

Source/Credit: Ural Federal University

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Black cardamom effective against lung cancer cells

NUS researchers embarked on a scientific study of black cardamom, a spice used in Indian Ayurvedic medicine, as a source of potent bioactive compounds that are effective against lung cancer cells. Source: National University of Singapore

The main challenges associated with existing lung cancer drugs are severe side effects and drug resistance. There is hence a constant need to explore new molecules for improving the survival rate and quality of life of lung cancer patients.

In Indian Ayurvedic medicine, black cardamom has been used in formulations to treat cancer and lung conditions. A team of researchers from the NUS Faculty of Science, NUS Yong Loo Lin School of Medicine, and NUS College of Design and Engineering studied the scientific basis behind this traditional medicinal practice and provided evidence of the cytotoxic effect of black cardamom on lung cancer cells. The research highlighted the spice as a source of potent bioactives, such as cardamonin and alpinetin, which could be used in the treatment or prevention of lung cancer. The study is the first to report the association of black cardamom extract with oxidative stress induction in lung cancer cells, and compare the spice’s effects on lung, breast and liver cancer cells.

The findings could potentially lead to the discovery of safe and effective new bioactives which can prevent or cure cancer formation. The research was first published in the Journal of Ethnopharmacology.

Analyzing sediments to investigate global warming occurring 56 million years ago

Aitor Payros
Credit: Unai Zorriketa. UPV/EHU

The Department of Geology of the UPV/EHU has examined sediments dating back 56 million years in the Tremp-Graus basin (on the border between Lleida and Huesca). It can be deduced from the study that the global warming episode at that time consisted of three phases in which the distribution of precipitation was different. The data from the study can be used to adjust mathematical models used to predict the effects of current climate change.

Major carbon emissions into the atmosphere and oceans took place 56 million years ago; that led to intense global warming known as the Paleocene-Eocene Thermal Maximum, and is regarded as an ancient analogue of today's anthropogenic warming. “Although the origin or cause of the warming at that time was different, the process was very similar to today’s warming, so it is considered to be similar to today's global warming. The climate is known to have warmed, but other alterations besides warming may occur with climate change. In particular, we wanted to analyze how the hydro-climatic conditions in terms of rainfall changed at that time,” said Aitor Payros, who gained a PhD in Geology at the UPV/EHU.

The UPV/EHU’s Department of Geology has investigated the mid-latitude alluvial and hydro-climatic changes recorded in the Tremp-Graus basin (on the border between Lleida and Huesca) during the Paleocene-Eocene Thermal Maximum, and has concluded that what happened then could in some way be similar to what is already happening today in the southeast of the Iberian Peninsula. To do this, they collected historical data from the region, and discovered geographical as well as hydro-climatic similarities.

Orchid helps insect get a grip

Figure 1: The white egret orchid (Habenaria radiata) resembles a dancing white egret.
Credit: Suetsugu Kenji / Kobe University

Scientific Frontline: "At a Glance" Summary

• Main Discovery: The elaborate, feather-like fringe of the white egret orchid (Habenaria radiata) functions primarily as a physical supportive platform that stabilizes hawkmoth pollinators during nectar feeding, rather than acting solely as a visual attractant.
• Methodology: Researchers conducted field experiments by surgically removing the petal fringes from specific plants in their natural habitat and performing detailed behavioral observations of hawkmoth interactions to measure visitation rates and subsequent seed viability.
• Key Data: Specimens with the fringe removed produced a significantly lower number of healthy seeds per fruit compared to intact plants, despite showing no decrease in the overall fruit production rate or pollinator visitation frequency.
• Significance: This study overturns the conventional evolutionary assumption that dramatic floral geometries are selected mainly for visual appeal, highlighting the critical role of physical flower-insect mechanics in driving floral diversity.
• Future Application: These findings provide essential data for biological conservation strategies, emphasizing the need to preserve specific functional morphological traits that facilitate mutualism in endangered wetland plant species.
• Branch of Science: Evolutionary Biology and Ecology
• Additional Detail: Contrary to the prior belief that hawkmoths hover continuously while feeding, behavioral analysis confirmed they actively grasp the orchid's fringe with their mid-legs to anchor themselves for effective pollen transfer.

New Optical Switch Could Lead to Ultrafast All-Optical Signal Processing

An artist's illustration of an optical switch, splitting
 light pulses based on their energies.
Credit: Y. Wang, N. Thu, and S. Zhou

Engineers at Caltech have developed a switch—one of the most fundamental components of computing—using optical, rather than electronic, components. The development could aid efforts to achieve ultrafast all-optical signal processing and computing.

Optical devices have the capacity to transmit signals far faster than electrical devices by using pulses of light rather than electrical signals. That is why modern devices often employ optics to send data; for example, think of the fiberoptic cables that provide much faster internet speeds than conventional Ethernet cables.

The field of optics has the potential to revolutionize computing by doing more, at faster speeds, and with less power. However, one of the major limitations of optics-based systems at present is that, at a certain point, they still need to have electronics-based transistors to efficiently process the data.

Now, using the power of optical nonlinearity (more on that later), a team led by Alireza Marandi, assistant professor of electrical engineering and applied physics at Caltech, has created an all-optical switch. Such a switch could eventually enable data processing using photons. The research was published in the journal Nature Photonics on July 28.

Switches are among the simplest components of a computer. A signal comes into the switch and, depending on certain conditions, the switch either allows the signal to move forward or halts it. That on/off property is the foundation of logic gates and binary computation, and is what digital transistors were designed to accomplish. However, until this new work, achieving the same function with light has proved difficult. Unlike electrons in transistors, which can strongly affect each other's flow and thereby cause "switching," photons usually do not easily interact with each other.

Octopus lures from the Marianas are the oldest in the world

UOG archaeologist Michael Carson at the 2013 excavation of Sanhalom in Tinian, near the House of Taga. The excavation uncovered an octopus lure artifact from a layer that Carson has since carbon dated to 1500–1100 B.C., making it the oldest known artifact of its kind in the world.
Credit: MARC | University of Guam

A University of Guam archaeological study has determined that cowrie-shell artifacts found throughout the Marianas were lures used for hunting octopuses and that the devices, which have been found on islands across the Pacific, are the oldest known artifacts of their kind in the world.

The study used carbon dating of archaeological layers to confirm that lures found in Tinian and Saipan were from about 1500 B.C., or 3,500 years ago.

“That’s back to the time when people were first living in the Mariana Islands. So, we think these could be the oldest octopus lures in the entire Pacific region and, in fact, the oldest in the world,” said Michael T. Carson, an archaeologist with the Micronesian Area Research Center at UOG.

The study, titled “Let’s catch octopus for dinner: Ancient inventions of octopus lures in the Mariana Islands of the remote tropical Pacific,” is published in World Archaeology, a peer-reviewed academic journal. Carson, who holds a doctorate in anthropology, is the lead author of the study, assisted by Hsiao-chun Hung from The Australian National University in Canberra, Australia.

The fishing devices were made with cowrie shells, a type of sea snail and a favorite food of octopuses, that were connected by a fiber cord to a stone sinker and a hook.

They have been found in seven sites in the Mariana Islands. The oldest lures were excavated in 2011 from Sanhalom near the House of Taga in Tinian and in 2016 from Unai Bapot in Saipan. Other locations include Achugao in Saipan, Unai Chulu in Tinian, and Mochom at Mangilao Golf Course, Tarague Beach, and Ritidian Beach Cave in Guam.

Bumblebees Appear to Feel Pain

Bees were given the choice between either unheated or noxiously-heated (55°C) feeders with different sucrose concentrations and marked by different colors.
Credit Pippa Ager

New research by a team at Queen Mary University of London shows that bumblebees can modify their response to ‘noxious’ (painful) stimuli in a manner that is viewed in other animals as consistent with the ability to feel pain.

The researchers showed that bumblebees are capable of modifying their response to ‘noxious’ (painful) stimuli in order to get a higher sugar reward. The possibility of insect pain and suffering should therefore be taken seriously, they say.

Queen Mary’s Professor Lars Chittka, author of the new book The Mind of a Bee, who led the research, said “Insects used to be regarded as simple reflex automatons, responding to damaging stimuli only by withdrawal reflexes. Our new work shows that bees’ responses are more flexible and that they can suppress such reflexes when it suits them, for example if there is an extra-sweet treat to be had. Such flexibility is consistent with the capacity of a subjective experience of pain”

Study first-author Matilda Gibbons, PhD student at Queen Mary University of London said, “Scientists traditionally viewed insects as unfeeling robots, which avoid injury with simple reflexes. We've discovered bumblebees respond to harm non-reflexively, in ways that suggest they feel pain. If insects can feel pain, humans have an ethical obligation not to cause them unnecessary suffering. But the UK's animal welfare laws don't protect insects - our study shows that perhaps they should.”

The brains of Neanderthals developed differently from those of modern humans

Fewer chromosome segregation errors in modern human than Neanderthal neural stem cells. Left side: microscopy image of the chromosomes (in cyan) of a modern human neural stem cell of the neocortex during cell division. Right side: same type of image, but of a cell where three amino acids in the two proteins KIF18a and KNL1, involved in chromosome separation, have been changed from the modern human to the Neanderthal variants. These “neanderthalized” cells show twice as many chromosomes separation errors (red arrow). 
Credit: Felipe Mora-Bermúdez / MPI-CBG

Neanderthals are the closest relatives to modern humans. The neocortex, the largest part of the outer layer of the brain, is unique to mammals and crucial for many cognitive capacities. Researchers from the Max Planck Institute of Molecular Cell Biology and Genetics in Dresden and the Max Planck Institute for Evolutionary Anthropology in Leipzig have now discovered that neural stem cells – the cells from which neurons in the developing neocortex derive – spend more time preparing their chromosomes for division in modern humans than in Neanderthals. This results in fewer errors when chromosomes are distributed to the daughter cells in modern humans than in Neanderthals or chimpanzees, and could have consequences for how the brain develops and functions.

After the ancestors of modern humans split from those of Neanderthals and Denisovans, their Asian relatives, about one hundred amino acids, the building blocks of proteins in cells and tissues, changed in modern humans and spread to almost all modern humans. The biological significance of these changes is largely unknown. However, six of those amino acid changes occurred in three proteins that play key roles in the distribution of chromosomes, the carriers of genetic information, to the two daughter cells during cell division.

A paper battery with water switch

The paper battery is composed of two electrochemical cells – at both ends of the paper strip – separated by a water barrier (between the letters "m" and "p") and connected in series.
Credit: Empa

A team of researchers at Empa developed a water-activated disposable paper battery. The researchers suggest that it could be used to power a wide range of low-power, single-use disposable electronics – such as smart labels for tracking objects, environmental sensors and medical diagnostic devices – and minimize their environmental impact. The proof-of-principle study has been published in the journal Scientific Reports.

The battery, devised by Gustav Nyström and his team, is made of at least one cell measuring one centimeter squared and consisting of three inks printed onto a rectangular strip of paper. Salt, in this case simply sodium chloride or table salt, is dispersed throughout the strip of paper and one of its shorter ends has been dipped in wax. An ink containing graphite flakes, which acts as the positive end of the battery (the cathode), is printed onto one of the flat sides of the paper while an ink containing zinc powder, which acts as the negative end of the battery (the anode), is printed onto the reverse side of the paper. Yet another ink containing graphite flakes and carbon black is printed on both sides of the paper, on top of the other two inks. This ink makes up the current collectors connecting the positive and negative ends of the battery to two wires, which are located at the wax-dipped end of the paper.

When a small amount of water is added, the salts within the paper dissolve and charged ions are released, thus making the electrolyte ionically conductive. These ions activate the battery by dispersing through the paper, resulting in zinc in the ink at the anode being oxidized thereby releasing electrons. By closing the (external) circuit these electrons can then be transferred from the zinc-containing anode – via the graphite- and carbon black-containing ink, the wires and the device – to the graphite cathode where they are transferred to – and hence reduce – oxygen from ambient air. These redox reactions (reduction and oxidation) thus generate an electrical current that can be used to power an external electrical device.