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Signs of Covid-19 may be hidden in speech signals
Studying voice recordings of infected but asymptomatic people reveals potential indicators of Covid-19.
Maybe their voices are lower or have a nasally tone. Infections change the quality of our voices in various ways. But MIT Lincoln Laboratory researchers are detecting these changes in Covid-19 patients even when these changes are too subtle for people to hear or even notice in themselves.
By processing speech recordings of people infected with Covid-19 but not yet showing symptoms, these researchers found evidence of vocal biomarkers, or measurable indicators, of the disease. These biomarkers stem from disruptions the infection causes in the movement of muscles across the respiratory, laryngeal, and articulatory systems. A technology letter describing this research was recently published in IEEE Open Journal of Engineering in Medicine and Biology.
While this research is still in its early stages, the initial findings lay a framework for studying these vocal changes in greater detail. This work may also hold promise for using mobile apps to screen people for the disease, particularly those who are asymptomatic.
"I had this 'aha' moment while I was watching the news," says Thomas Quatieri, a senior staff member in the laboratory's Human Health and Performance Systems Group. Quatieri has been leading the group's research in vocal biomarkers for the past decade; their focus has been on discovering vocal biomarkers of neurological disorders such as amyotrophic lateral sclerosis (ALS) and Parkinson's disease. These diseases, and many others, change the brain's ability to turn thoughts into words, and those changes can be detected by processing speech signals.
He and his team wondered whether vocal biomarkers might also exist for Covid-19. The symptoms led them to think so. When symptoms manifest, a person typically has difficulty breathing. Inflammation in the respiratory system affects the intensity with which air is exhaled when a person talks. This air interacts with hundreds of other potentially inflamed muscles on its journey to speech production. These interactions impact the loudness, pitch, steadiness, and resonance of the voice — measurable qualities that form the basis of their biomarkers.
While watching the news, Quatieri realized there were speech samples in front of him of people who had tested positive for Covid-19. He and his colleagues combed YouTube for clips of celebrities or TV hosts who had given interviews while they were Covid-19 positive but asymptomatic. They identified five subjects. Then, they downloaded interviews of those people from before they had Covid-19, matching audio conditions as best they could.
They then used algorithms to extract features from the vocal signals in each audio sample. "These vocal features serve as proxies for the underlying movements of the speech production systems," says Tanya Talkar, a PhD candidate in the Speech and Hearing Bioscience and Technology program at Harvard University.
The signal's amplitude, or loudness, was extracted as a proxy for movement in the respiratory system. For studying movements in the larynx, they measured pitch and the steadiness of pitch, two indicators of how stable the vocal cords are. As a proxy for articulator movements — like those of the tongue, lips, jaw, and more — they extracted speech formants. Speech formants are frequency measurements that correspond to how the mouth shapes sound waves to create a sequence of phonemes (vowels and consonants) and to contribute to a certain vocal quality (nasally versus warm, for example).
They hypothesized that Covid-19 inflammation causes muscles across these systems to become overly coupled, resulting in a less complex movement. "Picture these speech subsystems as if they are the wrist and fingers of a skilled pianist; normally, the movements are independent and highly complex," Quatieri says. Now, picture if the wrist and finger movements were to become stuck together, moving as one. This coupling would force the pianist to play a much simpler tune.
The researchers looked for evidence of coupling in their features, measuring how each feature changed in relation to another in 10 millisecond increments as the subject spoke. These values were then plotted on an eigenspectrum; the shape of this eigenspectrum plot indicates the complexity of the signals. "If the eigenspace of the values forms a sphere, the signals are complex. If there is less complexity, it might look more like a flat oval," Talkar says.
In the end, they found a decreased complexity of movement in the Covid-19 interviews as compared to the pre-Covid-19 interviews. "The coupling was less prominent between larynx and articulator motion, but we're seeing a reduction in complexity between respiratory and larynx motion," Talkar says.
These preliminary results hint that biomarkers derived from vocal system coordination can indicate the presence of Covid-19. However, the researchers note that it's still early to draw conclusions, and more data are needed to validate their findings. They're working now with a publicly released dataset from Carnegie Mellon University that contains audio samples from individuals who have tested positive for Covid-19.
Beyond collecting more data to fuel this research, the team is looking at using mobile apps to implement it. A partnership is underway with Satra Ghosh at the MIT McGovern Institute for Brain Research to integrate vocal screening for Covid-19 into its VoiceUp app, which was initially developed to study the link between voice and depression. A follow-on effort could add this vocal screening into the How We Feel app. This app asks users questions about their daily health status and demographics, with the aim to use these data to pinpoint hotspots and predict the percentage of people who have the disease in different regions of the country. Asking users to also submit a daily voice memo to screen for biomarkers of Covid-19 could potentially help scientists catch on to an outbreak.
"A sensing system integrated into a mobile app could pick up on infections early, before people feel sick or, especially, for these subsets of people who don't ever feel sick or show symptoms," says Jeffrey Palmer, who leads the research group. "This is also something the U.S. Army is interested in as part of a holistic Covid-19 monitoring system." Even after a diagnosis, this sensing ability could help doctors remotely monitor their patients' progress or monitor the effects of a vaccine or drug treatment.
As the team continues their research, they plan to do more to address potential confounders that could cause inaccuracies in their results, such as different recording environments, the emotional status of the subjects, or other illnesses causing vocal changes. They're also supporting similar research. The Mass General Brigham Center for COVID Innovation has connected them to international scientists who are following the team's framework to analyze coughs.
"There are a lot of other interesting areas to look at. Here, we looked at the physiological impacts on the vocal tract. We're also looking to expand our biomarkers to consider neurophysiological impacts linked to Covid-19, like the loss of taste and smell," Quatieri says. "Those symptoms can affect speaking, too."
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A man's skeleton, found facedown with his hands bound, was unearthed near an ancient ceremonial circle during a high speed rail excavation project.
- A skeleton representing a man who was tossed face down into a ditch nearly 2,500 years ago with his hands bound in front of his hips was dug up during an excavation outside of London.
- The discovery was made during a high speed rail project that has been a bonanza for archaeology, as the area is home to more than 60 ancient sites along the planned route.
- An ornate grave of a high status individual from the Roman period and an ancient ceremonial circle were also discovered during the excavations.
An ancient skeleton of a man dating back to the Iron Age was uncovered outside of London last month, and though archaeologists aren't certain what the cause of death was, clues point to a murder most foul.
A skeleton representing a man who was tossed face down into a ditch nearly 2,500 years ago with his hands bound in front of his hips was dug up during a high speed rail excavation.
The positioning of the remains have led archaeologists to suspect that the man may have been a victim of an ancient murder or execution. Though any bindings have since decomposed, his hands were positioned together and pinned under his pelvis. There was also no sign of a grave or coffin.
"He seems to have had his hands tied, and he was face-down in the bottom of the ditch," said archaeologist Rachel Wood, who led the excavation. "There are not many ways that you end up that way."
Currently, archaeologists are examining the skeleton to uncover more information about the circumstances of the man's death. Fragments of pottery found in the ditch may offer some clues as to exactly when the man died.
"If he was struck across the head with a heavy object, you could find a mark of that on the back of the skull," Wood said to Live Science. "If he was stabbed, you could find blade marks on the ribs. So we're hoping to find something like that, to tell us how he died."
Other discoveries at Wellwick Farm
The grim discovery was made at Wellwick Farm near Wendover. That is about 15 miles north-west of the outskirts of London, where a tunnel is going to be built as part of a HS2 high-speed rail project due to open between London and several northern cities sometime after 2028. The infrastructure project has been something of a bonanza for archaeology as the area is home to more than 60 ancient sites along the planned route that are now being excavated before construction begins.
The farm sits less than a mile away from the ancient highway Icknield Way that runs along the tops of the Chiltern Hills. The route (now mostly trails) has been used since prehistoric times. Evidence at Wellwick Farm indicates that from the Neolithic to the Medieval eras, humans have occupied the region for more than 4,000 years, making it a rich area for archaeological finds.
Wood and her colleagues found some evidence of an ancient village occupied from the late Bronze Age (more than 3,000 years ago) until the Roman Empire's invasion of southern England about 2,000 years ago. At the site were the remains of animal pens, pits for disposing food, and a roundhouse — a standard British dwelling during the Bronze Age constructed with a circular plan made of stone or wood topped with a conical thatched roof.
Ceremonial burial site
A high status burial in a lead-lined coffin dating back to Roman times.
Photo Credit: HS2
While these ancient people moved away from Wellwick Farm before the Romans invaded, a large portion of the area was still used for ritual burials for high-status members of society, Wood told Live Science. The ceremonial burial site included a circular ditch (about 60 feet across) at the center, and was a bit of a distance away from the ditch where the (suspected) murder victim was uncovered. Additionally, archaeologists found an ornately detailed grave near the sacred burial site that dates back to the Roman period, hundreds of years later when the original Bronze Age burial site would have been overgrown.
The newer grave from the Roman period encapsulated an adult skeleton contained in a lead-lined coffin. It's likely that the outer coffin had been made of wood that rotted away. Since it was clearly an ornate burial, the occupant of the grave was probably a person of high status who could afford such a lavish burial. However, according to Wood, no treasures or tokens had been discovered.
Sacred timber circle
An aerial view of the sacred circular monument.
Photo Credit: HS2
One of the most compelling archaeological discoveries at Wellwick Farm are the indications of a huge ceremonial circle once circumscribed by timber posts lying south of the Bronze Age burial site. Though the wooden posts have rotted away, signs of the post holes remain. It's thought to date from the Neolithic period to 5,000 years ago, according to Wood.
This circle would have had a diameter stretching 210 feet across and consisted of two rings of hundreds of posts. There would have been an entry gap to the south-west. Five posts in the very center of the circle aligned with that same gap, which, according to Wood, appeared to have been in the direction of the rising sun on the day of the midwinter solstice.
Similar Neolithic timber circles have been discovered around Great Britain, such as one near Stonehenge that is considered to date back to around the same time.
This spring, a U.S. and Chinese team announced that it had successfully grown, for the first time, embryos that included both human and monkey cells.
In the novel, technicians in charge of the hatcheries manipulate the nutrients they give the fetuses to make the newborns fit the desires of society. Two recent scientific developments suggest that Huxley's imagined world of functionally manufactured people is no longer far-fetched.
On March 17, 2021, an Israeli team announced that it had grown mouse embryos for 11 days – about half of the gestation period – in artificial wombs that were essentially bottles. Until this experiment, no one had grown a mammal embryo outside a womb this far into pregnancy. Then, on April 15, 2021, a U.S. and Chinese team announced that it had successfully grown, for the first time, embryos that included both human and monkey cells in plates to a stage where organs began to form.
As both a philosopher and a biologist I cannot help but ask how far researchers should take this work. While creating chimeras – the name for creatures that are a mix of organisms – might seem like the more ethically fraught of these two advances, ethicists think the medical benefits far outweigh the ethical risks. However, ectogenesis could have far-reaching impacts on individuals and society, and the prospect of babies grown in a lab has not been put under nearly the same scrutiny as chimeras.
Mouse embryos were grown in an artificial womb for 11 days, and organs had begun to develop.
Growing in an artificial womb
When in vitro fertilization first emerged in the late 1970s, the press called IVF embryos “test-tube babies," though they are nothing of the sort. These embryos are implanted into the uterus within a day or two after doctors fertilize an egg in a petri dish.
Before the Israeli experiment, researchers had not been able to grow mouse embryos outside the womb for more than four days – providing the embryos with enough oxygen had been too hard. The team spent seven years creating a system of slowly spinning glass bottles and controlled atmospheric pressure that simulates the placenta and provides oxygen.
This development is a major step toward ectogenesis, and scientists expect that it will be possible to extend mouse development further, possibly to full term outside the womb. This will likely require new techniques, but at this point it is a problem of scale – being able to accommodate a larger fetus. This appears to be a simpler challenge to overcome than figuring out something totally new like supporting organ formation.
The Israeli team plans to deploy its techniques on human embryos. Since mice and humans have similar developmental processes, it is likely that the team will succeed in growing human embryos in artificial wombs.
To do so, though, members of the team need permission from their ethics board.
CRISPR – a technology that can cut and paste genes – already allows scientists to manipulate an embryo's genes after fertilization. Once fetuses can be grown outside the womb, as in Huxley's world, researchers will also be able to modify their growing environments to further influence what physical and behavioral qualities these parentless babies exhibit. Science still has a way to go before fetus development and births outside of a uterus become a reality, but researchers are getting closer. The question now is how far humanity should go down this path.
Chimeras evoke images of mythological creatures of multiple species – like this 15th-century drawing of a griffin – but the medical reality is much more sober. (Martin Schongauer/WikimediaCommons)
Human–monkey hybrids might seem to be a much scarier prospect than babies born from artificial wombs. But in fact, the recent research is more a step toward an important medical development than an ethical minefield.
If scientists can grow human cells in monkeys or other animals, it should be possible to grow human organs too. This would solve the problem of organ shortages around the world for people needing transplants.
But keeping human cells alive in the embryos of other animals for any length of time has proved to be extremely difficult. In the human-monkey chimera experiment, a team of researchers implanted 25 human stem cells into embryos of crab-eating macaques – a type of monkey. The researchers then grew these embryos for 20 days in petri dishes.
After 15 days, the human stem cells had disappeared from most of the embryos. But at the end of the 20-day experiment, three embryos still contained human cells that had grown as part of the region of the embryo where they were embedded. For scientists, the challenge now is to figure out how to maintain human cells in chimeric embryos for longer.
Regulating these technologies
Some ethicists have begun to worry that researchers are rushing into a future of chimeras without adequate preparation. Their main concern is the ethical status of chimeras that contain human and nonhuman cells – especially if the human cells integrate into sensitive regions such as a monkey's brain. What rights would such creatures have?
However, there seems to be an emerging consensus that the potential medical benefits justify a step-by-step extension of this research. Many ethicists are urging public discussion of appropriate regulation to determine how close to viability these embryos should be grown. One proposed solution is to limit growth of these embryos to the first trimester of pregnancy. Given that researchers don't plan to grow these embryos beyond the stage when they can harvest rudimentary organs, I don't believe chimeras are ethically problematic compared with the true test–tube babies of Huxley's world.
Few ethicists have broached the problems posed by the ability to use ectogenesis to engineer human beings to fit societal desires. Researchers have yet to conduct experiments on human ectogenesis, and for now, scientists lack the techniques to bring the embryos to full term. However, without regulation, I believe researchers are likely to try these techniques on human embryos – just as the now-infamous He Jiankui used CRISPR to edit human babies without properly assessing safety and desirability. Technologically, it is a matter of time before mammal embryos can be brought to term outside the body.
While people may be uncomfortable with ectogenesis today, this discomfort could pass into familiarity as happened with IVF. But scientists and regulators would do well to reflect on the wisdom of permitting a process that could allow someone to engineer human beings without parents. As critics have warned in the context of CRISPR-based genetic enhancement, pressure to change future generations to meet societal desires will be unavoidable and dangerous, regardless of whether that pressure comes from an authoritative state or cultural expectations. In Huxley's imagination, hatcheries run by the state grew a large numbers of identical individuals as needed. That would be a very different world from today.
Sahotra Sarkar, Professor of Philosophy and Integrative Biology, The University of Texas at Austin College of Liberal Arts
Scientists should be cautious when expressing an opinion based on little more than speculation.
- In October 2017, a strange celestial object was detected, soon to be declared our first recognized interstellar visitor.
- The press exploded when a leading Harvard astronomer suggested the object to have been engineered by an alien civilization.
- This is an extraordinary conclusion that was based on a faulty line of scientific reasoning. Ruling out competing hypotheses doesn't make your hypothesis right.
Sometimes, when you are looking for something ordinary, you find the unexpected. This is definitely the case with the strange 'Oumuamua, which made international headlines as a potential interstellar visitor. Its true identity remained obscure for a while, as scientists proposed different explanations for its puzzling behavior. This is the usual scientific approach of testing hypotheses to make sense of a new discovery.
What captured the popular imagination was the claim that the object was no piece of rock or comet, but an alien artifact, designed by a superior intelligence.
Do you remember the black monolith tumbling through space in the classic Stanley Kubrick movie 2001: A Space Odyssey? The one that "inspired" our ape-like ancestors to develop technology and followed humanity and its development since then? What made this claim amazing is that it wasn't coming from the usual UFO enthusiasts but from a respected astrophysicist from Harvard University, Avi Loeb, and his collaborator Shmuel Bialy. Does their claim really hold water? Were we really visited by an alien artifact? How would we know?
A mystery at 200,000 miles per hour
Before we dive into the controversy, let's examine some history. 'Oumuamua was discovered accidentally by Canadian astronomer Robert Weryk while he was routinely reviewing images captured by the telescope Pan-STARRS1 (Panoramic Survey and Rapid Response System 1), situated atop the ten-thousand-foot Haleakala volcanic peak on the Hawaiian island of Maui. The telescope scans the skies in search of near-Earth objects, mostly asteroids and possibly comets that come close to Earth. The idea is to monitor the solar system to learn more about such objects and their orbits and, of course, to sound the alarm in case of a potential collision course with Earth. Contrary to the objects Weryk was used to seeing, mostly moving at about 40,000 miles per hour, this one was moving almost five times as fast — nearly 200,000 miles per hour, definitely an anomaly.
Intrigued, astronomers tracked the visitor while it was visible, concluding that it indeed must have come from outside our solar system, the first recognized interstellar visitor. Contrary to most known asteroids that move in elliptical orbits around the sun, 'Oumuamua had a bizarre path, mostly straight. Also, its brightness varied by a factor of ten as it tumbled across space, a very unusual property that could be caused either by an elongated cigar shape or by it being flat, like a CD, one side with a different reflectivity than the other. The object, 1I/2017 U1, became popularly known as 'Oumuamua, from the Hawaiian for "scout."
In their paper, Loeb and Bialy argue that the only way the object could be accelerated to the speeds observed was if it were extremely thin and very large, like a sail. They estimated that its thickness had to be between 0.3 to 0.9 millimeters, which is extremely thin. After confirming that such an object is robust enough to withstand the hardships of interstellar travel (e.g., collision with gas particles and dust grains, tensile stresses, rotation, and tidal forces), Loeb and Bialy conclude that it couldn't possibly be a solar system object like an asteroid or comet. Being thus of interstellar origin, the question is whether it is a natural or artificial object. This is where the paper ventures into interesting but far-fetched speculation.
I'm not saying it was aliens, but it was aliens
First, the authors consider that it might be garbage "floating in interstellar space as debris from advanced technological equipment," ejected from its own stellar system due to its non-functionality; essentially, alien space junk. Then, they suggest that a "more exotic scenario is that 'Oumuamua may be a fully operational probe sent intentionally to Earth vicinity by an alien civilization," [italicized as in the original] concluding that a "survey for lightsails as technosignatures in the solar system is warranted, irrespective of whether 'Oumuamua is one of them."
You can shoot down as many hypotheses as you want to vindicate yours, but this doesn't prove yours is the right one.
I have known Avi Loeb for decades and consider him a serious and extremely talented astrophysicist. His 2018 paper includes a suggestive interpretation of strange data that obviously sparks the popular imagination. Theoretical physicists routinely suggest the existence of traversable wormholes, multiverses, and parallel quantum universes. Not surprisingly, Loeb was highly in demand by the press to fill in the details of his idea. A book followed, Extraterrestrial: The First Sign of Intelligent Life Beyond Earth, and its description tells all: "There was only one conceivable explanation: the object was a piece of advanced technology created by a distant alien civilization."
This is where most of the scientific establishment began to cringe. One thing is to discuss the properties of a strange natural phenomenon and rule out more prosaic hypotheses while suggesting a daring one. Another is to declare to the public that the only conceivable explanation is one that is also speculative. An outsider will conclude that a reliable scientist has confirmed not only the existence of extraterrestrial life but of intelligent and technologically sophisticated extraterrestrial life with an interest in our solar system. I wonder if Loeb considered the impact of his words and how they reflect on the scientific community as a whole.
This is why aliens won't talk to us
Earlier this year, in a live public lecture hosted by the Catholic University of Chile, Avi Loeb locked horns with Jill Tarter, the scientist that is perhaps most identifiable as someone who spent her career looking for signs of extraterrestrial intelligence. (Coincidentally, I was the speaker that followed Loeb the next week in the same seminar series and was cautioned — along with the other panelists — to behave myself to avoid another showdown. I smiled, knowing that my topic was pretty tame in comparison. I mean, how can the limits of human knowledge compare with alien surveillance?)
The Loeb-Tarter exchange was awful and, it being a public debate, was picked up by the press. Academics can be rough like anyone else. But the issue goes deeper.
What scientists say matters. When should a scientist make public declarations about a cutting-edge topic with absolute certainty? I'd say never. There is no clear-cut certainty in cutting-edge science. There are hypotheses that should be tested more until there is community consensus. Even then, consensus is not guaranteed proof. The history of science is full of examples where leading scientists were convinced of something, only to be proven wrong later.
The epistemological mistake Loeb committed was to make an assertion that publicly amounted to certainty by using a process of elimination of other competing hypotheses. You can shoot down as many hypotheses as you want to vindicate yours, but this doesn't prove yours is the right one. It only means that the other hypotheses are wrong. I do, however, agree with Loeb when he says that 'Oumuamua should be the trigger for an increase in funding for the search for technosignatures, a way of detecting intelligent extraterrestrial life.