Author Archives: Nancy Cohen

About Nancy Cohen

Nancy Cohen is a writer from Cambridge, MA. She holds an MS from Columbia University Graduate School of Journalism. Her focus is on business, science, and technology.

Not your sister’s art hobby: DNA origami can save lives

Increasingly, origami (the Japanese art of paper folding) is becoming less of an artistic concern and more of a scientific one. The California Institute of Technology made special news in 2006 about a way to weave DNA strands into any two-dimensional shape or figure. Caltech’s Paul Rothemund called it “DNA origami” — but that was just the start of it.

Image credits: Nikoline Arns.

Imagine strands of DNA folded back and forth, forming a scaffold that fills the outline of a desired shape. Then, imagine more DNA strands specially designed to bind to that scaffold.

Rothemund, the strand-weaver, explained why this was useful. Scientists would find it easy to create and study any complex nanostructures they might want. Quoted in a 2006 press release, in he said he came up with a half a dozen shapes, including square, triangle, five-pointed star, and smiley face.

“At this point, high-school students could use the design program to create whatever shape they desired,” Rothemund said at the time.

Nature News said the binders, DNA ‘staples,’ were short strands “that stop the viral strand from unraveling,” adding that the method could find use in molecular biology and electronics. “The technique could be used to build a flat scaffold to carry microscopic electronic components. Enzymes could also be attached, creating a tiny protein factory,” the article emphasized.

In 2016, Caltech shed new light on the discovery. “The publication of Paul Rothemund’s paper on DNA origami (Nature, March 16, 2006) marked a turning point in DNA nanotechnology, enabling unprecedented control over designed molecular structures.”

Step by step

DNA origami object from viral DNA visualized by electron tomography. Image credits: OrigamiMonkey / Wikipedia.

Well, it’s 2021 and better late than never. The latest news about DNA origami is that Jacob Majikes and Alex Liddle, researchers at the National Institute of Standards and Technology (NIST), having stayed with the topic of DNA origami for years, have compiled a detailed tutorial on the technique. “DNA Origami Design: A How-To Tutorial” has been published in the Journal of Research of the National Institute of Standards and Technology. Majikes and Liddle have provided a step-by-step guide on the design of DNA origami nanostructures, making it easier than ever to design and use this type of structure.

Over the years, the method had attracted hundreds of researchers, said NIST, and for various reasons: Some may be interested in order to detect and treat diseases, or, to assess pollutants’ impacts on the environment and other applications. The two guide authors explained what they did. Namely, they went for the ‘how.’

“We wanted to take all the tools that people have developed and put them all in one place, and to explain things that you can’t say in a traditional journal article,” said Majikes. “Review papers might tell you everything that everyone’s done, but they don’t tell you how the people did it.”

Their journal paper further stated what was needed:

While the design and assembly of DNA origami are straightforward, its relative novelty as a nanofabrication technique means that the tools and methods for designing new structures have not been codified as well as they have for more mature technologies, such as integrated circuits. While design approaches cannot be truly formalized until design-property relationships are fully understood, this document attempts to provide a step-by-step guide to designing DNA origami nanostructures using the tools available at the current state of the art.”

Many potential applications of DNA origami have been suggested in literature, including drug delivery systems and nanotechnological self-assembly of materials, so this is not just some ethereal approach, it has clinical use. For instance, Harvard University Wyss Institute researchers reported the self-assembling and self-destructing drug delivery vessels using the DNA origami in lab tests, and another team of researchers from China and the US created a DNA origami delivery vehicle for Doxorubicin, a commonly used anti-cancer drug. So when someone acts like origami is just cute art, tell them that’s not nearly the case — it could be a real lifesaver.

Bigger boost in robot’s field of view

Oregon State University’s team has earned some serious bragging rights: they’ve come up with an optical sensor that can mimic the human eye. Think of robots, ones that are built to track moving objects. Roboticists dealing with such machines wouldn’t have to play with complex image processing anymore — they could rely on this optical sensor to do the job.

The human eye, while not nearly as highly performant as some of its counterparts from the animal kingdom, is still a magnificent structure. Replicating its functionality in robots has proven immensely challenging, but the OSU team’s work brings us one step closer to it, as their robot eye is able to closely match the human eye’s ability to perceive changes in its visual field.

Due to the way the team’s sensor works, a static item in the robot’s field of view would draw no response. A moving object would—registering a high voltage. Science Focus summed up the importance of their work thusly:

“Currently, computers receive information in a step-by-step way, processing inputs as a series of data points, whereas this technology helps build a more integrated system. For artificial intelligence, researchers are attempting to build on human brains which contain a network of neurons, communicating cells, able to process information in parallel.”

For example, the OSU team proceeded to simulate an array of “retinomorphic” (human eye-type) sensors that predict how a retina-like video camera would respond to visual stimuli. The idea was to input videos into one of these arrays and process that information in the same way a human eye would. For instance, one such simulation shows a bird flying into view, then all but disappearing as it stops at an invisible bird feeder. The bird reappears as it takes off. The feeder, swaying, becomes visible only as it starts to move. But you don’t just need the eye, you also need the processing power — which in the case of humans, is provided by the brain. The OSU team also tried to replicate that.

The team’s paper appears in Applied Physics Letters, explaining that “neuromorphic computation is the principle whereby certain aspects of the human brain are replicated in hardware. While great progress has been made in this field in recent years, almost all input signals provided to neuromorphic processors are still designed for traditional (von Neumann) computer architectures.”

You may have already read about researchers exploring devices that behave like eyes, especially retinomorphic devices. But previous attempts to build a human-eye type of device relied on software or complex hardware, said John Labram, Assistant Professor of Electrical and Computing Engineering.

The Science Focus piece describes why he stepped up to this kind of research effort. Labram was “initially inspired by a biology lecture he played in the background, which detailed how the human brain and eyes work.” Our eyes are very sensitive to changes in light, the piece explains, but less responsive to constant illumination. This marked the core of a new approach for devices that mimic photo-receptors in our eyes.

The innovation in this work lies mostly in the materials and the technique they used. The authors discuss how “a simple photosensitive capacitor will inherently reproduce certain aspects of biological retinas.” Their design involves using ultrathin layers of perovskite semiconductors — perovskite being a mineral also used for solar panels, among others. The perovskite is a few hundred nanometers thick and works as a capacitor that varies capacitance under illumination.

These change from strong electrical insulators to strong conductors when exposed to light. “You can think of it as a single pixel doing something that would currently require a microprocessor,” said Labram, for the university’s news site.

Their human eye-like sensor would not just be useful for object tracking robots, though. Consider that “neuromorphic computers” belong to a next generation of artificial intelligence in applications like self-driving cars. traditional computers process information sequentially as a series of instructions; neuromorphic computers emulate the human brain’s massively parallel networks, said the OSU report.

Scientists leverage natural killer cells against lymphoma

A heavy layer of glycans, seen here in green, cover immune cells and provide a way to target cancer-specific markers in the body. Credit: Wu Lab, Scripps Research.

Lymphoma is a cancer that impacts lymphocytes (the white blood cells that form our body’s first line of immunity, defending the body from foreign invaders like bacteria and viruses). Lymphoma travels through the blood and lymphatic system, causing the lymphocytes to change and grow out of control.

Scientists want to find ways to treat patients with lymphoma and some are paying attention to what nature gives us to target cancers. These are the “natural killer cells.”

According to a study published in Nature Reviews Cancer on natural killer (NK) cells, cytotoxic innate lymphocytes are present at high frequency in the circulatory system. The report noted their “exquisite ability to spontaneously detect and lyse transformed or stressed cells.”

Now, researchers are developing treatments to activate NK cells using small molecules or cytokines, and even testing genetically modified living NK cells as therapies.

A suitable name

Philipp Eissmann, Imperial College, London, UK, discussed natural killer cells on the British Society for Immunology site. He said as cells of the innate immune system, NK cells respond quickly to a variety of pathological challenges. He also said that NK cells are best known for killing virally infected cells, and detecting and controlling early signs of cancer.

“NK cells were first noticed for their ability to kill tumor cells without any priming or prior activation (in contrast to cytotoxic T cells, which need priming by antigen-presenting cells). They are named for this ‘natural’ killing.”

Making news on this front is a Scripps Research Institute team, where the researchers have modified NK cells to target lymphoma. Their study, published in Angewandte Chemie, reports their attempts to modify the cells for cancer-fighting powers specifically against lymphoma.

This marks a departure from existing therapies, according to a study co-author, Peng Wu, who is an associate professor in the Department of Molecular Medicine at Scripps Research.

Sialyl-Lewis X

“Some existing lymphoma treatments, including B-cell-killing antibodies and so-called CAR-T cell therapies, work by targeting B cells indiscriminately, largely wiping them out. However, this strategy brings many adverse side effects, including months of immunosuppression due to low antibody levels,” notes a press release on Scripps Research.

The team worked to modify cells to concentrate cancer-fighting power against lymphoma. They added Sialyl-Lewis X, which made the cells gather in bone marrow amid the lymphoma cells. This led to a delay in the development of lymphoma in mice. Scripps referred to the Sialyl-Lewis X as “homing molecules,” indicating scientists’ interest in cell-based treatments that can enhance cancer-killing powers at the site of the cancer.

“Wu and his lab now are continuing to develop this and related strategies for clinical use,” the Scripps Research concludes.

Researchers try to figure out aphantasia: life without mental imagery

The inability to visualise images in one’s head is known as aphantasia. The letter ‘A’ indicates “without” and phantasia indicates the term coined by aristotle to indicate the “power by which a mental representation is presented to us”.

“In my mind’s eye” — it’s a nice conversation starter, but for some, it’s easier said than done. In fact, calling an image to mind is not possible for those suffering from a condition called aphantasia. Those suffering from this condition simply cannot conjure an image in their mind. While our “mind’s eye” normally allows a lot of us to see things in our head, they try to deliver the same effect with words or other non-visual ways.

Now a recent study on the topic sheds more light on how people with this condition perform on memory tasks. The study leader is Wilma Bainbridge, an expert in the neuroscience of perception and memory.

“Some individuals with aphantasia have reported that they don’t understand what it means to ‘count sheep’ before going to bed,” commented Wilma Bainbridge, an assistant professor of psychology at the University of Chicago.

Appearing in Cortex, this study used a set of visual memory tasks on study participants. Some were aphantasic individuals while others had typical imagery capabilities.

Bainbridge and team gave them photographs of three rooms. Participants had to draw each from memory and then, a second time, using the photograph as reference.

“Individuals with typical imagery usually drew the most salient objects in the room with a moderate amount of detail, like color and key design elements (a green carpet, rather than a rectangle),” according to a report from UChicago News.

Leaning on words

What about those with aphantasia? Different outcomes. Their drawings carried only a few objects, and the drawings were often simple. They leaned at times on written descriptions. Instead of windowpanes, for example, they wrote the word “window” inside an outline of a window.

Credit: University of Chicago.

Still, aphantasia does not negatively impact spatial memory. Study subjects with aphantasia were able to place the objects that they did remember in the correct location within a room most of the time, just like those with typical imagery.

As notable, people with aphantasia made fewer mistakes.

“They didn’t create any false memories of objects that hadn’t been in any of the rooms,” said UChicago News, “and placed objects in the correct location—but the wrong room—only three times.”

The ones with typical imagery made 14 mistakes on average and regularly included objects that had not even been in the photographs, like the person who drew a piano in a living room that had no piano. One strategy that the aphantasia subjects appear to rely on is what Bainbridge calls “verbal-coding of the space.” And this is what might actually give them an edge over those with more typical recall, in terms of avoiding false memories.

The scientific quest to better understand differences between those with aphantasia and people with traditional mind’s-eye capabilities is on.

Work choices

A report from BBC Science Focus in May said people with aphantasia were more likely to work in a STEM field — that is, more likely to work in scientific and mathematical industries than in creative sectors. That is what researchers found at the University of Exeter, and it came as a bit of a surprise at the time.

They tested 2,000 people with aphantasia, 200 with hyperphantasia and 200 control participants with mid-range imagery vividness. The research was led by the University of Exeter with collaborators from the University of Edinburgh and Heriot-Watt University.

What’s next: With co-authors, from University of Westminster and National Institute of Mental Health, Bainbridge is interested in exploring more about aphantasia as manifested in the brain. She wants to use MRI scanning “to elucidate some of the mechanisms behind imagery in typical and aphantasic individuals.”

Researchers stack travel thoughts in the moment with ‘write on-the-go’ app

LiveSnippets is a voice-based, multimedia journaling app that allows the user to verbally capture their thoughts, along with images and videos. Credit: National University of Singapore.

Thinking while you see and later seeing all that you thought, are the twin ideals for those who travel. Well, that’s the ideal way, but you know what really happens. You use your smartphone to click the image but too many of your thought bursts do just that–they burst and fly.

All those quirky jokes, those observations, those data bits, could be rolled into a perfect travel story that never or barely gets told. You had your bunch of photos and videos ready to go, but memory dims what you thought during that special time.

A PhD student in Singapore can attest to that. Hyeongcheol Kim went off to a computer conference in Montreal and was excited to make his own side journey to Quebec City, to take in its sights and vibe. His mind was on the conference after that, and when he tried to write about everything he wanted in his travel blog he realized his Quebec recall wasn’t good.

He wondered if there was an easy way to capture his thoughts and feelings in words with images real-time, rather than struggling with half-baked memories after returning home. Enter a challenge in “experience writing,” where, with the right solution, all those clever little thought burst don’t go away because they are captured in the moment, and without always whipping out a notepad and weighing down the moment. He talked about the challenge with Shengdong Zhao, head of the NUS Human-Computer Interaction lab; joining in were Can Liu and Kotaro Hara. Result: LiveSnippets, a voice-based multimedia journaling app designed to run on Android.

They discussed their work in a paper prepared as a conference presentation.

“LiveSnippets: Voice-based Live Authoring of Multimedia Articles about Experiences” was prepared for MobileHCI ’20: the 22nd International Conference on Human-Computer Interaction with Mobile Devices and Services.

Cognitive demands

They reminded readers why documenting experiences can be difficult.

Documenting experiences digitally in blogs and journals is a common activity that allows people to socially connect with others by sharing their experiences (e.g., travelogue). However, documenting such experiences can be time-consuming and cognitively demanding as it is typically done OUT-OF-CONTEXT (after the actual experience).”

How LiveSnippets works: You dictate thoughts about relevant photos and videos. You save them as a stack of editable snippets. The stack can be reordered. In other words, you would have a way to put the travel experience back into context. Another plus is that reluctant writers may have confidence, once they see their thoughts organized, to show the world and publish.

Recipes and product reviews

Hyeongcheol Kim (right) developed the Android app with his supervisor A/P Shengdong Zhao (left), and two other collaborators, after wondering if there could be an easier way to capture a user’s thoughts and feelings in real-time while travelling. Credit: National University of Singapore.

Kim said in the NUS news story that a user can use the app to generate an HTML file of the travel blog or social media post complete with pictures and captions, along with other details. You just publish with a click.

The NUS site said, “A user — say someone seeing the Eiffel Tower for the first time — pulls out his smartphone and starts to take pictures or videos. At the same time, he begins to describe what he sees, how he feels, and any other thoughts that comes to mind. The app captures all of this, along with contextual information such as time, date, and location, with a single press of a button. It also transcribes the user’s narration into text.”

Apart from travel, LiveSnippets can be used for other types of experiential writing. They tried out LiveSnippets using three scenarios: travel writing, creating recipes, and reviewing products.

How they tested: A small group with different writing backgrounds (expert and novice) were test participants. Each had to generate three snippets and use them to write an article based on one of those three scenarios. Results: Kim said the team was satisfied with results as they showed the feasibility of using LiveSnippets as an alternative way of writing articles.

What’s next?

The team is posing a new question: What if they can integrate LiveSnippets into smart glasses? While the app goes beyond just scribbling down words into a spiral notebook, they think that as a smart glasses tool, it could even beat having to use a mobile phone in the special moment.

The ‘loss-of-smell’ COVID-19 symptom probably matters more than you think

By now, everywhere you look, lists of COVID-19 symptoms are out there. The tell-tale symptom that stands out as a real bummer (especially for foodies) is the loss of taste and smell. What happens if you lose the two? The doors to a myriad every-day experiences slam shut. You can’t smell. You can’t taste. A big part of your life is temporarily gone.

Being unable to savor a stir-fry, though, is not the big problem here. It’s not just about not being able to smell or enjoy your favorite food, but this unusual symptom could have longer-lasting consequences, particularly in regards to mental health. Surgeons and behavioral scientists are concerned over the anxiety and depression that can accompany smell and taste disabilities because of COVID-19.

In turn, support groups for helping patients over hurdles of anxiety and depression have made themselves heard.
Groups like Fifth Sense and AbScent are helping people who have lost their sense of smell and taste, offering support for them. One person giving testimony of what it feels like without a sense of smell thought about missing the smell of newborns and fresh-cut grass, and that “gorgeous smell after the rain.”

Based in the UK, Fifth Sense carries convincing messages that losing your sense of smell is much more profound than you may think. Psychological consequences can be serious. In its deep-dive into the psychological impacts of smell loss, the site reminded its readers that smell is one of the ways we connect with the world.

“Anosmia sufferers often talk of feeling isolated and cut-off from the world around them, and experiencing a ‘blunting’ of the emotions,” the organization says.

Dr. Eric Mair, chief of otolaryngology with Sharp Rees-Stealy Medical Group, said research informs us that smell and taste are linked to our memories and emotions, and their loss “can lead to depressed mood and anxiety.”

Sandeep Datta, associate professor of neurobiology in the Blavatnik Institute at Harvard Medical School, said that anosmia (loss of smell) “can be devastating for the small fraction of people in whom it’s persistent.” He cautioned that we could be looking at a different public health problem if we have a growing population with a lasting loss of smell. Datta was the lead author of a study that indicated that the novel coronavirus changes the sense of smell in patients not by directly infecting neurons but by affecting the function of supporting cells. Their study appeared in Science Advances in July.

So, toss aside your disappointment over some cake. The anxiety is heightened by never knowing you might be predisposed to something deadly or harmful. What about not being able to smell something burning in your house? What about not sensing a gas leak? Or feeling unsure if you have any body odors?

Interestingly, observations about the loss of taste and smell as a symptom of COVID-19 were noticed as early as May this year, when a Vanderbilt University faculty member mentioned this symptom to colleagues. Justin Turner, associate professor of Otolaryngology-Head and Neck Surgery and medical director of Vanderbilt University Medical Center’s Smell and Taste Center, said it was not uncommon for patients with viral upper respiratory infections to experience a temporary — or sometimes permanent — loss of taste or smell.” He also said, “These symptoms appear to be particularly prevalent in COVID-19.”

Higher numbers

As the year 2020 winds to an end, it is still not certain the actual percentage of people hit with a loss of taste and smell as a result of COVID-19. Numbers have been all over the place, with some percentage citations as high as 80%; one systematic review said it was 62%.

Almost two-thirds of the people admitted to an Italian hospital with COVID-19 in March experienced losing their senses of smell and taste, according to a study published in the Dec. 9 online issue of Neurology, a journal of the American Academy of Neurology. Loss of smell and taste was present in 58 people, or 63% of the group. For 13 of the 58 participants (or 22%) the loss of smell and taste was their first symptom. The average duration of the loss of smell and taste was 25 to 30 days. In the Italy study, compared with corona virus-infected patients who had not lost their sense of smell and taste, the people with a compromised sense of smell had lower amounts of white blood cells, or leukocytes. A subset of white blood cells, neutrophils, was reduced. These cells help the body fight infection.

Study author Francesco Bax, of Santa Maria della Misericordia University Hospital in Udine, Italy, said, “For people whose first symptoms were loss of taste and smell, we found very few had nasal congestion, so we think obstruction of the nasal passages is an unlikely cause of these symptoms. However, the association between a blood cell imbalance and losing your sense of smell may help in identifying patients at risk.”

Short hauls and longer

While scientists raise their questions, victims ask how long will this taste and smell lockout last? Studies suggest that this symptom can last for up to four to six weeks, said Penn Medicine.

Dr. Mair, meanwhile, said, “While most people regain these senses after recovering from Covid-19, we are seeing some ‘long-haulers,’ or people who have symptoms for months, not regain their ability to smell and taste for extended periods of time.”

Some practitioners think that regularly smelling strong odors or essential odors may restore their olfactory system.

Bioprinting as a matter of the heart

A cross-disciplinary team of scientists at Carnegie Mellon University College of Engineering have just brought an ambitious what-if plan to fruition. The team has created a full-size 3D bio-printed human heart model.

Yes, it is just a model but, but it realistically mimics the elasticity of cardiac tissue and could be useful for medical research.

Image credits: CMU Engineering.

Those behind this model at Carnegie Mellon University (CMU) are Adam Feinberg and his team in the Departments of Biomedical Engineering and Materials Science and Engineering.

They managed to print this artificial heart through special bioprinting with a 3D printer, using custom materials and a technique called FRESH, which stands for Freeform Reversible Embedding of Suspended Hydrogels. Their 3D printer was custom made to hold a gel support bath large enough to print at the desired size and some software changes served to maintain the speed and fidelity of the print.

“FRESH 3D printing uses a needle to inject bioink into a bath of soft hydrogel,” said the school’s news story about the heart model, “which supports the object as it prints. Once finished, a simple application of heat causes the hydrogel to melt away, leaving only the 3D bioprinted object,” the researchers explain.

Jumping the hurdles

The work is a culmination of several years of research. Machine Design talked about what was new and what was not new about the Carnegie Mellon marker: Full-size organ models have been replicated before, using 3D printing techniques, but the materials had a tendency of not being ideal for replicating the “feel” and mechanical properties of natural tissue.

Now, this team was focused on getting the right materials to get the artificial structure to behave just like the real thing. They were aware that soft, tissue-like materials, such as silicone rubbers, often collapsed when 3D printed in air, making it difficult to reproduce large, complex structures.

They used something called alginate, a naturally occurring polymer, as the alginate could mimic the elastic modulus of cardiac tissues. Alginate is a soft, natural polymer, with properties similar to real cardiac tissue. They placed sutures in a piece of alginate to hold even when stretched. This suggested how surgeons could practice procedures on a heart model made from the alginate material.

That is just one potential application. Although hospitals might have facilities for 3D printing models of a patient’s body, the tissues and organs can currently only be modeled in hard plastic or rubber. The Carnegie model would enable manipulation in ways similar to a real heart.

Crticial steps taken

Feinberg is interested in working with surgeons and clinicians to fine-tune the technique and ensure readiness for a hospital setting.

The paper discussing their work has been published in ACS Biomaterials Science and Engineering. Lead author Eman Mirdamadi recognized that major hurdles still exist in bioprinting a full-sized functional human heart, but this is a foundational groundwork—and showing immediate applications for realistic surgical simulation.

Feinberg concludes:

“While we have not yet achieved printing a whole adult-sized functional heart, what we have done is really taken critical steps along that path.”

Numb and Nope obstruct vaccine efforts

In a world turned upside down by the pandemic, we’re following a lot of different threads: vaccine news, data graphics, infection hot spots, distribution issues, you name it. But… how are we doing, really? It’s hard to get an accurate sense of how the pandemic is going.

At the close of 2020, says Harvard T.H. Chan School of Public Health Dean Michelle Williams, we are at an inflection point. At a presentation called “COVID-19: Chasing Science to Save Lives,” she discussed the current opportunities and challenges brought by the vaccination campaigns that are just around the corner.

Williams says that on the plus side, news of vaccines really is promising. The mRNA technology has brought forth a whole new class of vaccines that are safe and quick to develop. But on the flip side, the pandemic is hitting a new spike and daily news is as bad as ever.

With all this news, one also can see how people can easily become numb.

Numbness is actually a major enemy in this pandemic. All across the country, we see footage of people in malls and at birthday parties, congregating without masks, without physical distancing, and with growing disinterest towards the pandemic.

“Is numbness the way we are coping?” she asked. It may very well be.

Resistance to science endangers all of us

What’s more, Williams (like all of us) has grappled with the fact that some of our leaders were so unwilling to follow the science. She said resistance to science was a clear and present danger to all of us.

The other danger is vaccine hesitancy. She referred to a Pew survey, where about 20 % of Americans said they were pretty certain that they would never take the vaccine no matter what new information they learned about it.

There are two main actors in this pandemic drama: scientists trying to find answers and the public who are free to accept or rebuff the answers. Scientists and the public need to work together. “We can’t work in silos,” she said. Establishing a good communication structure is even more important as this isn’t the first nor the last pandemic to pose a threat to mankind. “What we do means a lot to all the future global threats ahead of us.”

Williams also mentions what Napoleon famously said to his valet ahead of one battle. He said to dress him slowly because he was in a hurry. Sometimes, slowing down and assimilating things is the fastest way to protect ourselves and our loved ones. “We cannot afford to go numb.”

Some degree of normality

Dr. Anthony Fauci, director of the National Institute of Allergy and Infectious Diseases, was part of the presentation and he spoke of ways to get out of the pandemic. He said not getting vaccinated should not turn out to be the missing link in achieving success.

“What percentage of people in our society are going to be willing to be vaccinated? If we have a 95% effective vaccine and only 40 to 50% of people in society get vaccinated, it’s going to take quite a while to get to that blanket of herd immunity that’s going to protect us enough that you and I would feel comfortable in going out into society and saying the level of virus is so low that its not a threat to anyone.”

Fauci believes if vaccinations are done efficiently enough over the second quarter of 2021, “by the time we get to the end of the summer, i.e., the third quarter, we may actually have enough herd immunity protecting our society that, as we get to the end of 2021, we can approach very much some degree of normality that is close to where we were before.”

A recent webinar featuring scientists in epidemiology had similarly commented that a hurdle to success would be vaccine hesitancy. The view was that if the vulnerable among the elderly and other communities refused to take vaccines when available, the battle to eradicate Covid-19 would not go far.

Barry Bloom, research professor of public health and former dean of the faculty, Harvard T.H. Chan School of Public Health, moderated. “Let me just say there’s a mantra,” said Bloom, among immunologists and vaccine people that “vaccines do not save lives. Vaccination does.”

Diamondback terrapin threatened by traffickers, new report notes

Wildlife trafficking has become such a major problem that conservationists are warning that many species are now at risk of extinction due to it. Not only that, but experts warn that wildlife trafficking increases the risk of “zoonotic” diseases jumping from animals to humans.

The diamondback terrapin. Image credits: Ryan Hagerty.

The year currently winding down wasn’t just a tough one for us, but also for most creatures on Earth, due to increasing threats. You can assume conservationists have their work cut out for 2021, especially given how an ever-increasing number of animals is threatened by extinction (and the threats aren’t always clear-cut).

That said, it is no surprise that the Center for Biological Diversity sounded a Dec. 18 alarm in the form of a news release over the diamondback terrapin and revealed a new report that talks about trafficking.

This terrapin turtle is one of 10 species highlighted by the Center that are falling in numbers and even disappearing from some areas in its habitat. The report from the Endangered Species Coalition notes that “Wildlife trafficking is a lucrative business, raking in an estimated $7 to $23 billion every year.”

Eggs for life

The terrapins have always had their problems — being hit by cars or drowning in crab traps — but trade and trafficking are posing significant threats. Only a small number of eggs hatch and survive to adulthood, so it is important for adult terrapins to live long lives and have the opportunity to lay many eggs, said the report, “Trafficked: 10 Species Threatened by the Wildlife Trade.”

Yes, these small turtles are cute. No, they should not be your home’s trinkets or menu items for foodies.

“Through the mid-1800s into the 20th century, terrapin soup surged in popularity in the United States,” said the ‘Trafficked’ report, “resulting in staggering harvests. While that soup largely disappeared from dinner tables, the terrapin’s population never rebounded.”

The turtles have speckled skin and they get their name from their diamond patterned shells. They are the only turtles in the world living exclusively in semi-salty waters of estuaries. “It is thought to be a keystone species in those ecosystems,” said the Center.

“Terrapins eat small fish and invertebrates with relatively soft shells, like aquatic snails and fiddler crabs,” notes the Trafficked report, adding that Females often have stronger jaws and can eat hard-shelled mollusks. These terrapins play an important ecosystem role as they are top predators in estuaries and are therefore crucial in protecting salt marsh ecosystem functions.

Elise Bennett, a staff attorney at the Center for Biological Diversity, commented that given its importance, “Wildlife officials should end wild trapping and crack down on traffickers to ensure a bright future for this rare little turtle.”

Trapping for trade

Some poachers snatching up wild terrapins have indeed been apprehended by wildlife officials. Several states have taken action, though, either to protect the terrapins against commercial trade or to put an end to commercial terrapin trapping — but much more is needed to ensure that their numbers don’t continue to dwindle.

The matter is all the more ironic since humans, an intelligent and highly developed species, don’t need terrapins or their eggs for sustenance, so why would a human need to snatch animals from their natural habitats? That is a question for exploring in other essays, but at least the Endangered Species Coalition provides a report overview that sums up where the world stands in terms of threats to species.

Several listed in the report are part of a global pet trade. Examples are the yellow-headed parrot and the Tokay gecko. Then there are the people who seek the animals out for food or medicinal reasons like the scalloped hammerhead shark, pinto abalone, and the pangolin. Thirdly, there are the attention seekers who desire “collectables,” including the Venus flytrap and the rufous hummingbird.

Robot workspace to get human touch remotely

It’s been fairly easy for some to adopt a remote working model during the pandemic, but manufacturing and warehouse workers have had it rougher — some tasks just need people to be physically present in the workplace.

But now, one team is working on a solution for the traditional factory floor that could allow more workers to carry out their labor from home.

The proposed human-in-the-loop assembly system. The robot workspace can be manipulated remotely. Image credits: Columbia Engineering.

Columbia Engineering announced that researchers have won a grant to develop the project titled “FMRG: Adaptable and Scalable Robot Teleoperation for Human-in-the-Loop Assembly.” The project’s raw ingredients include machine perception, human-computer interaction, human-robot interaction, and machine learning.

They have come up with a “physical-scene-understanding algorithm” to convert visual observations via camera shots of a robot workspace into a virtual 3D-scene representation.  

Handling 3D models

The system analyzes the robot worksite and can change it into a visual physical scene representation. Each object is represented by a 3D model that mimics its shape, size, and physical attributes. A human operator gets to specify the assembly goal by manipulating these virtual 3D models.

A reinforcement learning algorithm infers a planning policy, given the task goals and the robot configuration. Also, this algorithm can infer its probability of success and use it to determine when to request human assistance — otherwise, it carries out its work automatically.

The project is led by Shuran Song, an assistant professor of computer science at Columbia University. She said the system they envision will allow workers who are not trained roboticists to operate the robots and this pleases her.

“I am excited to see how this research could eventually provide greater job access to workers regardless of their geographical location or physical ability.”

Automation for the future

The team received $3.7m funding from the National Science Foundation (NSF). The NSF stated the award period starts from January 1 to an estimated end date of Dec. 31, 2025. The NSF award abstract reveals the positive impact such an effort could have on business and workers:

“The research will benefit both the manufacturing industry and the workforce by increasing access to manufacturing employment and improving working conditions and safety. By combining human-in-the-loop design with machine learning, this research can broaden the adoption of automation in manufacturing to new tasks. Beyond manufacturing, the research will also lower the entry barrier to using robotic systems for a wide range of real-world applications, such as assistive and service robots.”

The abstract said their team is collaborating with NYDesigns and LaGuardia Community College “to translate research results to industrial partners and develop training programs to educate and prepare the future manufacturing workforce.”

Song is directing the vision-based perception and machine learning algorithm designs for the physical-scene-understanding algorithms. Computer Science Professor Steven Feiner, Columbia University, is looking at the 3D and VR user interface. Matei Ciocarlie, associate professor of mechanical engineering, Columbia University, is building the robot learning and control algorithms. Before joining the faculty, Matei was a scientist at Willow Garage, and scientist at Google. Matei contributed to the development of the open-source Robot Operating System.

A takeaway: News of robots often results in hair-pulling remarks on a tradeoff that can result in lost jobs for humans. Here is a project that, once complete, has the potential to complement human capabilities by using robotics.

Nancy Cohen is a contributing author. Want to get involved like Nancy and send your story to ZME Science? Check out our contact and contribute page.

What’s killing people around the world

Headlines dealing with ‘Health’ have inevitably been filled with COVID-19 stats. It’s understandable. We want to try to understand as much as possible about this killer beast that. But the pandemic isn’t the only thing killing people.

A new report by the World Health Organization (WHO) quantified what has killed pepeople in 2020. According to their finds, the top 10 killers are responsible for more than of half of the entire toll.

What’s killing people and how

Stepping off the COVID-19 info treadmill for a moment might not be such a bad idea, especially if it gives us the time to assess what the World Health Organization reports as the top causes of death and disability worldwide from 2000 to 2019.

According to WHO’s 2019 Global Health Estimates, published on Dec. 9, noncommunicable diseases made up seven of the world’s top ten causes of death. The top killer, however, was heart disease.

The world’s biggest killer was ischaemic heart disease, responsible for 16% of the world’s deaths. “Since 2000, the largest increase in deaths has been for this disease, rising by more than 2 million to 8.9 million deaths in 2019,” the report mentions. Ischemia is defined as a condition in which the blood flow and oxygen are restricted or reduced. The American Heart Association says that cardiac ischemia refers to decreased blood flow and oxygen to the heart muscle.

Overall, the top global causes of death were grouped into three categories: cardiovascular (ischaemic heart disease, stroke), respiratory (chronic obstructive pulmonary disease, lower respiratory infections), and neonatal conditions like birth asphyxia and birth trauma, neonatal sepsis and infections, and preterm birth complications.

In terms of wealth

The WHO report further looked at diseases vis a vis income levels. In high-income countries, deaths due to Alzheimer’s disease and other dementias were on the rise, surpassing stroke as the second leading cause.

In upper-middle-income countries, deaths from lung cancer rose: “stomach cancer featured highly in upper-middle-income countries compared to the other income groups, remaining the only group with this disease in the top 10 causes of death,” the WHO explains.

Communicable diseases, meanwhile, showed troubling numbers in low-income countries. Six of the top 10 causes of death in low-income countries were communicable diseases.

“People living in a low-income country are far more likely to die of a communicable disease than a noncommunicable disease,” said the WHO report. This is also perhaps why so many developed countries found it difficult to deal with the pandemic — they were not used to dealing with infectious diseases recently.

The pandemic has only shown even more just how important and difficult it is to maintain accurate datasets of this nature.

“COVID-19 has highlighted the importance for countries to invest in civil registration and vital statistics systems to allow daily counting of deaths, and direct prevention and treatment efforts. It has also revealed inherent fragmentation in data collection systems in most low-income countries, where policy-makers still do not know with confidence how many people die and of what causes,” said the WHO.

Pandemic forecast

Jason Beaubien of NPR News reflected on the time of the report’s data, through 2019 — before COVID-19 was known to be the global threat that it has become.

“So far this year,” said Beaubien, COVID has killed more than 1.5 million people. Forecasters predict that by the end of this year, the pandemic’s death toll could rise to 1.9 million.”

If so, COVID-19 would surely occupy a place on the list of the most deadly diseases.

The organization is stepping up to make sure detailed, accurate information is available on how many people die and of what cause, hoping to encourage rapid mortality surveillance.

Given the tools to support rapid mortality surveillance, the idea is that countries can collect data on the number of deaths by day, week, sex, age, and location. This can help health leaders deliver more timely efforts.

Ocean warming is a wrecking ball for coral reef systems. This researcher wants to understand it all

Year in and year out, scientist Thomas DeCarlo saw the writing on the wall — the wall of coral reefs, that is — and his findings are sounding the alarm: ocean warming and acidification could spell doom for coral reef ecosystems.

Coral reefs are vital for the health of the oceans. Image credits: Olga Tsai.

Billion-dollar buffers

“Ocean temperatures are now approaching one degree above what they were in industrial times, with a projected increase of two to four degrees, which could have terrible consequences for corals,” DeCarlo says.

DeCarlo has studied the history of monsoon upwelling, wind patterns, and other weather factors affecting coral reef ecosystems in the Red Sea. His research shows that reefs are essential not just to the corals themselves, but to the entire surrounding ecosystems, and human society as well.

If reefs collapse, so too do biodiverse life systems that rely on them to survive — and the damage will continue to cascade. Coral reefs are a nursery to different marine species, they provide fish for humans, and they buffer shores from storms.

That storm-buffer feature is apparently quite significant in dollars. In a US Geological Survey report, coral reef barriers as a force in flood protection protect $1.8 billion worth of coastal infrastructure and economic activity in the US and trust territories alone. Reefs reduce the energy of the waves as they wash ashore, which prevents or limits coastal erosion, flooding, and water surges.

DeCarlo’s detailed explorations use microsope, climate models, coral cores, and computerized tomography (CT) analysis, to study the relationship between climate stressors, bleaching, and calcification. He’s not the first scientist to study the environmental impact of coral reefs but he has taken a special look at instances where the upwelling of nutrient levels can be toxic to corals.

Composite photo shows samples of coral cores alongside CT scans of coral skeletal cores showing annual pairs of light and dark bands of high and low density. Photo: Thomas DeCarlo.

His plan, he says, is to build a global database of the history of coral bleaching events, helping to fill the gaps in our knowledge of coral resilience and vulnerability. But to do that, we first need to understand how the climate is affecting corals.

High, hot, and deadly

Winds blowing across the ocean surface push water away. Water then rises up from beneath the surface to replace the water that was pushed away, a process known as “upwelling,” explains the National Ocean Service (NOS). The water that rises to the surface is typically colder and is rich in nutrients, which “fertilize” surface waters, and have high biological productivity.

For corals, upwelling can be a blessing or a curse. According to DeCarlo knows, nutrient-dense waters can spell good news or bad news. It depends.

“Summer monsoons circulate nutrient-dense waters from the Gulf of Aden to the Red Sea. The symbiotic algae that live in corals thrive on these nutrients. In return, they provide food and energy for the corals to grow,” said DeCarlo. “But warmer waters create more nutrients, which create more algae, which create more oxygen and waste build-up in corals. When high waste conditions combine with high heat, this situation causes bleaching, which could turn deadly.”

According to the NOS, bleaching events might or might not be a dire threat for coral. If stress caused bleaching is not severe, the coral may recover. But if (1) there is prolonged algae loss and (2) continued stress, coral eventually dies.

There’s much work to be done, and DeCarlo has no intentions of stopping anytime soon. From King Abdullah University of Science and Technology (KAUST) and now on to Hawaii, at Hawaii Pacific University, his work offered valuable insight into the life of corals, but there’s much more research to be done, especially in regards to global warming. DeCarlo’s website states that “global warming is driving an increase in the frequency of mass coral bleaching events worldwide.”

Healthy coral reef and marine life in the central Red Sea of Saudi Arabia. Photo: KAUST.

It took the researcher 4 years to finish his PhD studying corals, an accomplishment he says he is “especially proud of,” since it was a first of its kind comprehensive study.

One important takeaway from this research is that coral reef environments are not a cookie-cutter affair. One-sized conclusions and conservation measures cannot address and fix everything. One must recognize the complexities due to what are the oceanographic settings of any individual coral reef.

Disentangling these oceanographic processes will help us predict when and where we may find coral reefs that are relatively resistant to rising temperatures, and this information will be critical to informing local management decisions.”

Stalkerware, the latest privacy threat groups vow to fight

A Nov. 26 report in Israel Defense reported that digital security company Avast named stalkerware as one of the main cyber threats of 2020 along with other threats such as COVID-19 scams, deepfakes, phishing attacks and ransomware. It said the malware was “typically installed secretly on mobile phones by so-called friends, jealous spouses and partners, ex-partners, and even concerned parents.”

In response, special groups have been springing up all over the place to fight this type of digital abuse. A stunning case in point: Coalition Against Stalkware (CAS), an anti-abuse group which recently celebrated its one-year anniversary.

The group has grown from strength to strength: it doubled its membership and joined partners such as mobile security companies and other organizations working to protect users’ safety. Ruzana Meretukova, a CAS author, marked the coalition’s one-year occasion by summing up key findings along the way.

For starters, the attacks of this nature are on the rise. In 2019, Kaspersky detected a 67% year-on-year increase of stalkerware usage on its users’ mobile devices at a global level. The number of stalkerware installations worldwide during the first 10 months of 2020 (from January to October) totaled more than 48,500, close to the total (almost 52,000 installations) over the same period in 2019.

The pandemic has also had an impact on the numbers. Meretukova says there was a rise in stalkerware detections starting back in March. So, what does this group do to counter stalkerware? Activities include speeches, publications, research, and collecting cybersecurity vendor data on stalkerware.

Defining the enemy

Another important contribution from the group is simply coming up with a precise definition of what exactly is stalkerware. So, what is it?

The Coalition’s definition sought to flesh out the concept referring to any app or program that does invade or is perceived to invade a person’s privacy, and a definition rather than the use of phrases that have made the rounds like ‘spouseware’ or ‘creepware.’

They ultimately define stalkerware as “software, made available directly to individuals, that enables a remote user to monitor the activities on another user’s device without that user’s consent and without explicit, persistent notification to that user in a manner that may facilitate intimate partner surveillance, harassment, abuse, stalking, and/or violence.”

Identifying stalkerware

Kaspersky Lab emphasized that people should not only know what it is is but also be proactive by recognizing signals that spell trouble.

While symptoms are not definite proof, it doesn’t hurt to trust your gut feeling (especially if it’s backed by a few clues) and make a safety plan. “Part of this safety plan could be to reach out to organizations working with victims of domestic violence,” Kaspersky notes.

Some of the common symptoms Kaspersky Daily listed as indicating the possibility of stalkerware on a device:

  • A battery that drains fast.
  • Overheating that’s constant.
  • Resets that were not prompted.
  • A big rise in mobile data use.
  • If others recently had physical access to your phone.
  • Applications with suspicious access to GPS tracking and other personal activities.

One anti-stalkerware tool recently was presented in Memeburn. That tool is called TinyCheck, which leans on Raspberry Pi and is open source. The good news: The perpetrator cannot tell you were putting it to work, yet it can detect any stalkerware installed on your phone or tablet.

TinyCheck is an open-source tool that relies on Rasberry Pi. It can detect stalkerware and spyware installed on smartphones and tablets, without making the perpetrator aware that such a check is being carried out. TinyCheck was developed by Félix Aimé, a security researcher, and it is available for free on GitHub for everyone to access.

Whether we like it or not, it looks like we’ll be spending a lot more time working remotely from home. Being aware of problems such as stalkerware and taking protective measures is definitely a part of a healthy online hygiene.