biology (30)

Planes, Trains, and Automobiles...

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Topics: Biology, COVID-19, Research

With COVID-19 reaching the most dangerous levels the U.S. has seen since the pandemic began, the country faces a problematic holiday season. Despite the risk, many people are likely to travel using various forms of transportation that will inevitably put them in relatively close contact with others. Many transit companies have established frequent cleaning routines, but evidence suggests that airborne transmission of the novel coronavirus poses a greater danger than surfaces. The virus is thought to be spread primarily by small droplets, called aerosols, that hang in the air and larger droplets that fall to the ground within six feet or so. Although no mode of public transportation is completely safe, there are some concrete ways to reduce risk, whether on an airplane, train or bus—or even in a shared car.

At a casual glance, air travel might seem like the perfect recipe for COVID transmission: it packs dozens of people into a confined space, often for hours at a time. But many planes have excellent high-efficiency particulate air (HEPA) filters that capture more than 99 percent of particles in the air, including microbes as SARS-CoV-2, the coronavirus that causes COVID. When their recirculation systems are operating, most commercial passenger jets bring in outside air in a top-to-bottom direction about 20 to 30 times per hour. This results in a 50–50 mix of outside and recirculated air and reduces the potential for the airborne spread of a respiratory virus. Many airlines now require passengers to wear a mask during flights except for mealtimes, and some are blocking off middle seats to allow more distancing between people. Companies have also implemented rigorous cleaning procedures between flights. So how does this translate into overall risk?

“An airplane cabin is probably one of the most secure conditions you can be in,” says Sebastian Hoehl of the Institute for Medical Virology at Goethe University Frankfurt in Germany, who has co-authored two papers on COVID-19 transmission on specific flights, which were published in JAMA Network Open and the New England Journal of Medicine, respectfully. Still, a handful of case studies have found that limited transmission can take place on board. One such investigation of a 10-hour journey from London to Hanoi starting on March 1 found that 15 people were likely infected with COVID-19 in-flight—and that 12 of them had sat within a couple of rows of a single symptomatic passenger in business class. (The results were published this month in the U.S. Centers for Disease Control and Prevention’s journal Emerging Infectious Diseases.) Most of these flights occurred early on in the pandemic, however, and in the case of the March 1 flight, masks were likely not worn, the researchers wrote. Meanwhile, a recent Department of Defense study modeled the risk of in-flight infection using mannequins exhaling simulated virus particles and found that a person would have to be exposed to an infectious passenger for at least 54 hours to get an infectious dose. This finding assumes the infected passenger is wearing a surgical mask, however, and it does not account for the dangers involved in removing the mask for meals or talking or in moving about on the plane.

Evaluating COVID Risk on Planes, Trains, and Automobiles, Sophie Bushwick, Tanya Lewis, Amanda Montañez, Scientific American

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COVID, and Math...

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Image Source: Link below

Topics: Biology, Chemistry, COVID-19, Mathematics, Physics

The year 2020 has been defined by the COVID-19 pandemic: The novel coronavirus responsible for it has infected millions of people and caused more than a million deaths. Like HIV, Zika, Ebola, and many influenza strains, the coronavirus made the evolutionary jump from animals to humans before wreaking widespread havoc. The battle to control it continues. When a disease outbreak is identified—usually through an anomalous spike in cases with similar symptoms—scientists rush to understand the new illness. What type of microbe causes the infection? Where did it come from? How does the infection spread? What are its symptoms? What drugs could treat it? In the current epidemic, science has proceeded at a frenetic pace. Virus genomes are quickly sequenced and analyzed, case and death numbers are visualized daily, and hundreds of preprints are shared every day.

Some scientists rush for their microscopes and lab coats to study a new infection; others leap for their calculators and code. A handful of metrics can characterize a new outbreak, guide public health responses, and inform complex models that can forecast the epidemic’s trajectory. Infectious disease epidemiologists, mathematical biologists, biostatisticians, and others with similar expertise try to answer several questions: How quickly is the infection spreading? What fraction of transmission must be blocked to control the spread? How long is someone infectious? How likely are infected people to be hospitalized or die?

Physics is often considered the most mathematical science, but theory and rigorous mathematical analysis also underlie ecology, evolutionary biology, and epidemiology.1 Ideas and people constantly flow between physics and those fields. In fact, the idea of using mathematics to understand infectious disease spread is older than germ theory itself. Daniel Bernoulli of fluid-mechanics fame devised a model to predict the benefit of smallpox inoculations2 in 1760, and Nobel Prize-winning physician Ronald Ross created mathematical models to encourage the use of mosquito control to reduce malaria transmission.3 Some of today’s most prolific infectious disease modelers originally trained as physicists, including Neil Ferguson of Imperial College London, an adviser to the UK government on its COVID-19 response, and Vittoria Colizza of Sorbonne University in Paris, a leader in network modeling of disease spread.

This article introduces the essential mathematical quantities that characterize an outbreak, summarizes how scientists calculate those numbers, and clarify the nuances in interpreting them. For COVID-19, estimates of those quantities are being shared, debated, and updated daily. Physicists are used to distilling real-world complexity into meaningful, parsimonious models, and they can serve as allies in communicating those ideas to the public.

The math behind epidemics, Alison Hill, Physics Today

Alison Hill is an assistant professor in the Institute for Computational Medicine and the infectious disease dynamics group at Johns Hopkins University in Baltimore, Maryland. She is also a visiting scholar at Harvard University in Cambridge, Massachusetts.

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Communication...

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Topics: Biology, COVID-19, Politics, Research

Living through a pandemic has resulted in phrases like RT-PCR, immune response, and aerosolized droplets becoming part of the regular vocabulary for a portion of the population. It has also underscored the important role that we all have to play as scientists in communicating science to the public. As research related to COVID-19 has moved forward at unprecedented rates, misinformation has also multiplied and spread at a terrifying pace. And no matter where you stand politically, all of this happening in an election year for the US further underscores the ways in which science has become an increasingly partisan issue.

Did I mention that the holidays are also approaching? While gatherings of family and friends may look different this year, you may still be anticipating a challenging conversation over a holiday meal with someone who has different viewpoints from yours.

Our situation comes with innumerable challenges. However, it also provides an opportunity for scientists to make a powerful contribution to society and demonstrate the value of science education. Whether or not you are engaging in research directly related to COVID-19, you can help those around you separate facts from myths, interpret the data that are available, and make better-informed decisions.

This realization occurred to me this spring. As positive cases of COVID-19 were just starting to appear in the US, I found myself talking to my physical therapist about the virus and potential treatments. Although I don’t work in drug development, I understand enough of the chemistry to know how nucleoside analogs such as the drug remdesivir function. I excitedly explained how viruses are sloppier than normal human cells when replicating their genomes and how researchers can capitalize on this to make drugs. A few days later, I found myself having a similar conversation with my mom. I wasn’t in a place to predict the efficacy of any drug, but I could at least explain why antivirals like remdesivir had a shot at working, while hydroxychloroquine was less promising. After these two conversations, it struck me that I could also share this knowledge with a broader population on social media.

Science communication is a skill that takes practice to develop, and I am still learning and growing. The stakes couldn’t be higher, but the important part is that any scientist can build this capability to communicate effectively.

We’re all science communicators. Here’s how to do it better, Jen Heemstra, Chemical & Engineering News

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Clusters...

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Image Source: Link below

Topics: Biology, COVID-19, Research

Continued: It triggered a big outbreak. At least 97 people who attended the conference, or lived in a household with someone who did, tested positive.

The Biogen meeting had become a superspreading event. Eventually, the virus spread from the meeting across Massachusetts and to other states. A recent study estimates it led to tens of thousands of cases in the Boston area alone.

Superspreading

COVID-19 superspreading events have been reported around the world. They happen in all sorts of places: bars and barbecues, gyms and factories, schools and churches, and on ships.

And even at the White House.

But why do these disease clusters occur—and why are they so important?

The reproduction rate

COVID-19 and many other diseases transmit from person to person. The reproduction rate, R, determines how fast a disease can spread.

R denotes the number of people infected, on average, by a single infected person. If R is 2, the number of cases doubles in every generation: from one infected person to two, to four, to eight, and so on.

The Science of Superspreading, Martin Enserink, Kai Kupferschmidt, and Nirja Desai, Science Magazine

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Modeling Spread...

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Image Source: Coronavirus and COVID-19: What You Should Know (WebMD)

Topics: Biology, Computer Modeling, COVID-19, Research

TOKYO (Reuters) – A Japanese supercomputer showed that humidity can have a large effect on the dispersion of virus particles, pointing to heightened coronavirus contagion risks in dry, indoor conditions during the winter months.

The finding suggests that the use of humidifiers may help limit infections during times when window ventilation is not possible, according to a study released on Tuesday by research giant Riken and Kobe University.

The researchers used the Fugaku supercomputer to model the emission and flow of virus-like particles from infected people in a variety of indoor environments.

Air humidity of lower than 30% resulted in more than double the amount of aerosolized particles compared to levels of 60% or higher, the simulations showed.

The study also indicated that clear face shields are not as effective as masks in preventing the spread of aerosols. Other findings showed that diners are more at risk from people to their side compared to across the table, and the number of singers in choruses should be limited and spaced out.

Japan supercomputer shows humidity affects aerosol spread of coronavirus, Rocky Swift, Reuters Science

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Quantum Dots and Diffusion...

QD tracking

Topics: Biology, Diffusion, Quantum Dots, Quantum Mechanics

Quantum dots diffuse within living cells in a nearly two-dimensional fashion. This result, which was obtained using a new 3D microscopy technique that can track single particles, sheds fresh light on intracellular diffusion – a process that is critical for moving molecules around the cell and for mediating other important activities. According to study leader Hui Li, a biophysicist at the Chinese Academy of Sciences in Beijing and Beijing Normal University, the 2D motion he and his colleagues observed is robust and stems from the complex architectures of the flat “adherent” biological cells they studied.

Quantum dots make ideal probes for studying intracellular diffusion in living cells. They are similar in size to intracellular macromolecules and can be made to mimic biological materials relatively easily, by coating their surfaces with organic molecules. Previous studies, however, relied mainly on two-dimensional measurements of their movement, with the assumption that three-dimensional diffusion is an extension of 2D diffusion and is isotropic.</em>

Quantum dots track two-dimensional diffusion in cellsIsabelle Dumé, Physics World

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ATCG Drive...

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MGM/VICTOR TANGERMANN

 

Topics: Biology, Computer Science, DNA

Why cannot we write the entire 24 volumes of the Encyclopedia Britannica on the head of a pin? Dr. Richard P. Feynman, "There's Plenty of Room at the Bottom," said to be the seminal talk that started the concept of atomic-level engineering, soon known as nanotechnology, (named by Professor Norio Taniguchi, 1974, of the Tokyo Science University).

The intricate arrangement of base pairs in our DNA encodes just about everything about us. Now, DNA contains the entirety of “The Wonderful Wizard of Oz” as well.

A team of University of Texas Austin scientists just vastly improved the storage capacity of DNA and managed to encode the entire novel — translated into the geek-friendly language of Esperanto — in a double strand of DNA far more efficiently than has been done before. DNA storage isn’t new, but this work could help finally make it practical.

Big tech companies like Microsoft are already exploring DNA-storage technology, as the biomolecule can encode several orders of magnitude more information per unit volume than a hard drive. But DNA is particularly error-prone. It can easily be damaged and erase whatever’s stored on it.

“The key breakthrough is an encoding algorithm that allows accurate retrieval of the information even when the DNA strands are partially damaged during storage,” molecular biologist Ilya Finkelstein said in a UT Austin press release.

Scientists Stored "The Wizard of Oz" on a Strand of DNA, Dan Robitzgi, Futurism

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Photonic Nanojets...

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FIG. 1. (a) Long-legs cellar spider. (b) Reeling mechanism. (c) Manufacturing process of decorating spider silk. (d) Spider silk with dome lens placed on a dedicated holder. (e) Microphotograph of dome lens. (f) Laser scanning digital microscope system for measuring dome lens. (g) Schematic diagram of the dome lens for generating PNJ.

 

Topics: Biology, Materials Science, Nanotechnology

ABSTRACT

In this work, we thoroughly investigate the shape, size, and location of the photonic nanojets (PNJs) generated from the illuminated dome lens. The silk fiber is directly extracted from the cellar spider and used to form the dome lens by its liquid-collecting ability. The solidified dielectric dome lenses with different dimensions are obtained by using ultraviolet curing. Numerical and experimental results show that the long PNJs are strongly modulated by the dimension of the dome lens. The optimal PNJ beam shaping is achieved by using a mesoscale dielectric dome lens. The PNJ with a long focal length and a narrow waist could be used to scan over a target for large-area imaging. The silk fiber with a dome lens is especially useful for bio-photonic applications by combining its biocompatibility and flexibility.

Optimal photonic nanojet beam shaping by mesoscale dielectric dome lens

Journal of Applied Physics 127, 243110 (2020); https://doi.org/10.1063/5.0007611

C.B. Lin, Yi-Ting Lee, and Cheng-Yang Liu

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A Scaffold in Time...

 

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A lattice scaffold 3D printed directly onto soft living tissue. (Courtesy: Ohio State University)

 

 

Topics: 3D Printing, Bioengineering, Biofabrication, Biology, Tissue Engineering

Tissue engineering is an emerging field in which cells, biomaterials and biotechnologies are employed to replace or regenerate damaged or diseased tissues. Currently, this is achieved by generating a biomaterial scaffold outside of the body, maturation in a bioreactor and then surgically implanting the created tissue into the patient. This surgery, however, poses the added risk of infection, increases recovery time and may even negate the therapeutic benefits of the implant.

To prevent such complications, a US research team is developing a way to fabricate 3D tissue scaffolds inside a living patient – so-called intracorporeal tissue engineering. The researchers, from the Terasaki Institute, Ohio State University and Pennsylvania State University, aim to use robotic direct-write 3D printing to dispense cell-laden biomaterials (bioinks) in a highly precise, programmable manner. The printed bioinks are delivered through minimally invasive surgical incisions and the body itself acts as the bioreactor for maturation.

Any technique used to directly print tissues inside the body, however, must meet a specific set of requirements. The biomaterial must be 3D printable at body temperature (37 °C), for example, and all procedural steps should not harm the patient. For example, current methods use UV light to crosslink the constructed tissue, which is not safe for use within the body.

To meet these requirements, the team produced a specially-formulated bioink designed for printing directly in the body. They used the hydrogel gelatin methacryloyl (GelMA) as the biomaterial, and introduced Laponite and methylcellulose as rheological modifiers to enhance printability. “This bio-ink formulation is 3D printable at physiological temperature, and can be crosslinked safely using visible light inside the body,” explains first author Ali Asghari Adib.

Tissue engineering moves closer to 3D printing inside the body, Tami Freeman, Physics World

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"A Whole New Universe"...

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A Cryo-EM map of the protein apoferritin. Credit: Paul Emsley/MRC Laboratory of Molecular Biology

 

Topics: Biology, Cryogenic-Electron Microscopy, Materials Science, Nanotechnology

A game-changing technique for imaging molecules known as cryo-electron microscopy has produced its sharpest pictures yet — and, for the first time, discerned individual atoms in a protein.

By achieving atomic resolution using cryogenic-electron microscopy (cryo-EM), researchers will be able to understand, in unprecedented detail, the workings of proteins that cannot easily be examined by other imaging techniques, such as X-ray crystallography.

The breakthrough, reported by two laboratories late last month, cements cryo-EM’s position as the dominant tool for mapping the 3D shapes of proteins, say scientists. Ultimately, these structures will help researchers to understand how proteins work in health and disease, and lead to better drugs with fewer side effects.

“It’s really a milestone, that’s for sure. There’s really nothing to break anymore. This was the last resolution barrier,” says Holger Stark, a biochemist and electron microscopist at the Max Planck Institute for Biophysical Chemistry in Göttingen, Germany, who led one of the studies1. The other2 was led by Sjors Scheres and Radu Aricescu, structural biologists at the Medical Research Council Laboratory of Molecular Biology (MRC-LMB) in Cambridge, UK. Both were posted on the bioRxiv preprint server on 22 May.

“True ‘atomic resolution’ is a real milestone,” adds John Rubinstein, a structural biologist at the University of Toronto in Canada. Getting atomic-resolution structures of many proteins will still be a daunting task because of other challenges, such as a protein’s flexibility. "These preprints show where one can get to if those other limitations can be addressed,” he adds.

‘It opens up a whole new universe’: Revolutionary microscopy technique sees individual atoms for first time

Ewen Callaway, Nature

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Salk, Sabin and the Sun...

Topics: Biology, COVID-19, History, Politics

On March 26, 1953, American medical researcher Dr. Jonas Salk announces on a national radio show that he has successfully tested a vaccine against poliomyelitis, the virus that causes the crippling disease of polio. In 1952—an epidemic year for polio—there were 58,000 new cases reported in the United States, and more than 3,000 died from the disease. For promising eventually to eradicate the disease, which is known as “infant paralysis” because it mainly affects children, Dr. Salk was celebrated as the great doctor-benefactor of his time.

Polio, a disease that has affected humanity throughout recorded history, attacks the nervous system and can cause varying degrees of paralysis. Since the virus is easily transmitted, epidemics were commonplace in the first decades of the 20th century. The first major polio epidemic in the United States occurred in Vermont in the summer of 1894, and by the 20th century thousands were affected every year. In the first decades of the 20th century, treatments were limited to quarantines and the infamous “iron lung,” a metal coffin-like contraption that aided respiration. Although children, and especially infants, were among the worst affected, adults were also often afflicted, including future president Franklin D. Roosevelt, who in 1921 was stricken with polio at the age of 39 and was left partially paralyzed. Roosevelt later transformed his estate in Warm Springs, Georgia, into a recovery retreat for polio victims and was instrumental in raising funds for polio-related research and the treatment of polio patients.

According to the link, the trials weren't without consequence:

In 1954, clinical trials using the Salk vaccine and a placebo began on nearly two million American schoolchildren. In April 1955, it was announced that the vaccine was effective and safe, and a nationwide inoculation campaign began. Shortly thereafter, tragedy struck in the Western and mid-Western United States, when more than 200,000 people were injected with a defective vaccine manufactured at Cutter Laboratories of Berkeley, California. Thousands of polio cases were reported, 200 children were left paralyzed and 10 died.

The Salk method - created in 1954 - is to inject inert forms of the virus into the bloodstream (made inactive with formaldehyde), then the body develops defenses, or antibodies against them, however it didn't prevent the virus from thriving in the intestines. His colleague, Dr. Sabin, injected an attenuated vaccine (1961), meaning it wasn't a fully inert strain so that the gut environment could be addresses. More here. The Sabin mostly eliminated Polio in the world, but the U.S. still uses the Salk method.

April 8, 1950, Mildred Dean married Robert H. Goodwin. Mom would earn an associates degree as a PN - practical nurse, and Pop worked for Hanes Dye and Finishing as an operator, under grueling conditions and few opportunities to promote until retirement. My big sister - in grade school at the time - would come along for the ride.

1954 - the year of the Polio vaccine, was also the date of Brown vs. Board of Education, where the Supreme Court reached a non-partisan, 9-0 decision, that education in America was separate and unequal.

1961 was the year the Sabin vaccine was created, and a couple who had been married twelve years got pregnant around Thanksgiving - I would be born August of 1962. I likely was beneficiary of the Sabin method at Kate Biting Hospital in Winston-Salem, NC, also the black hospital where my mother worked.

We cannot "patent the sun." But one can be grateful for the impact of invention by Dr. Salk and Dr. Sabin on the quality of life given to everyone in my generation, and forward, and African American parents wise enough to wait for it.

There will be a sunrise, past this moment.

Dr. Jonas Salk announces polio vaccine, History.com Editors

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Masks...

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People walk through Piazza Duomo in Milan on May 7th. Some restrictions were lifted this week in Italy.BY CARLO COZZOLI/SHUTTERSTOCK.

 

Topics: Biology, COVID-19, Mathematical Models

Though I likely look like an alarmist to some of my neighbors and most of Greensboro, I will be wearing masks for the duration of this pandemic and the release of a vaccine under hopefully, a more functional administration in 2021.

“I felt like this was pretty urgent,” said De Kai, who was born in St. Louis, and is the son of immigrants from China. “I saw the country where I grew up, where my family lives [now mostly in the Bay Area], about to face this pandemic without knowing much about something as simple as wearing a mask to protect themselves and others.” In part, this comes from a cultural difference between East Asia, where masks have been routinely worn for decades to fend off pollution and germs, and other parts of the world. This includes the U.S., where people are unaccustomed to wearing masks, and, in the past, have sometimes been insensitive, even stigmatizing East Asians, many of whom had chosen to wear them in public prior to the pandemic, and had continued the practice in the aftermath of the SARS and MERS outbreaks. (In part, this habit was meant to show other people that they were concerned about transmitting the disease—something we in the West would do well to emulate.)

De Kai’s solution, along with his team, was to build a computer forecasting model they call the masksim simulator. This allowed them to create scenarios of populations like those in Japan (that generally wear masks) and others (that generally don’t), and to compare what happens to infection rates over time. Masksim takes sophisticated programming used by epidemiologists to track outbreaks and pathogens like COVID-19, Ebola, and SARS, and blended this with other models that are used in artificial intelligence to take into account the role of chance, in this case the randomness and unpredictability, of human behavior—for instance, when a person who is infected decides to go to a beach. De Kai’s team have also added some original programming that takes into account mask-specific criteria, such as how effective certain masks are at blocking the invisible micro-droplets of moisture that spray out of our mouths when we exhale or speak, or our noses when we sneeze, which scientists believe are significant vectors for spreading the coronavirus.

If 80% of Americans Wore Masks, COVID-19 Infections Would Plummet, New Study Says, David Ewing Duncan, Vanity Fair

Here's the ArXiv preprint paper to review. It takes ninth grade reading comprehension. What you don't understand in terms can be discerned with a search engine.

What is not "exceptional," nor greatness is the threat of "getting beat up" (M. Signorile article) that an Austin man reported saying he felt simply complying with the simple, constitutional right of wearing a mask to protect others from the spread of a lethal virus. What is not "exceptional," nor greatness: threatening a sovereign state assembly in Minnesota with armed terrorists (that's the only word that comes to mind), and making a deal amounts to quid pro quo extortion! Nor is it normal Michigan State Rep. Sarah Anthony has to enlist armed citizens to protect her as she goes about her duties of governance.

The beginning of this four decade cluster fuck started with a simple phrase that became dogma and orthodoxy for republicans by their only patron saint, Ronald Reagan:

In his inaugural address after taking the oath of office on January 20, Ronald Reagan called upon Americans to "begin an era of national renewal." In response to the serious problems facing the country, both foreign and domestic, he asserted his familiar campaign phrase: "Government is not the solution to our problem, government is the problem." He hoped that America "will again be the exemplar of freedom and a beacon of hope for those who do not have freedom."

The Ronald Reagan Presidential Library & Museum

It has thus devolved to Orange Satan's comment by Stephen-lost-to-Jews-forever-Miller, noted by Dahlia Lithwick in Slate: “This American carnage stops right here and stops right now,” was simply the inauguration of the same; a preamble to depravity. It has devolved into the irony of lock down protesters spreading the very virus they travel hundreds of miles to protest: then, take their bodies and arms back home after not social distancing from possibly asymptomatic brethren to "hug grandma." It has been government by past midnight Tweet, ineptitude on steroids, bungled pandemic response, bullying threats, racist innuendo; stoked nationalism and xenophobia. Any outside observer would say "United States" is an oxymoron, led by a fucking moron. An electoral victory won't magically solve our problems. We'll be wearing masks for a while until we get an actual treatment protocol and vaccine. "Normal" is a relative term. We haven't gone back to walking loved ones to their planes, we haven't stopped taking off our shoes nor have we repented of invasive body scans since and after 9/11. We won't go back to "normal" anymore other than science fiction, where we can travel to the past, glorified or not.

At least the mask of "exceptionalism" has permanently been removed, replaced by red hats and armed terrorists. There is no room for doubt of our full depravity. My vote in November will be to end this, and Damnatio Memoriae: a fitting end to a narcissist.

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Group Screening...

 

Topics: Biology, COVID-19, Statistics

Unless there is widespread testing for COVID-19, experts warn, cases will surge as governments reopen more businesses and public spaces. But there is still a woeful shortage of diagnostic tests for coronavirus infections, because of unprecedented demand for chemicals and supplies. The U.S., for instance, does hundreds of thousands of tests a day, but that number is still far short of the millions of daily assays recommended for a safe return to normal.

Now dozens of researchers in the U.S., Israel and Germany are pursuing a strategy to dramatically increase diagnostic capacity: group tests. By pooling samples from many people into a few groups and evaluating pools rather than individuals, the scientists think they can use fewer tests on more people. This approach could lead to the faster detection of individuals who are unwitting carriers of the disease and an ability to quickly clear others who have not been infected. The strategy has been used in the past to successfully detect cases of HIV, chlamydia, malaria and influenza, and was originally conceived during World War II to test thousands of military personnel for syphilis.

“As long as we have no vaccine, we can only stop the transmission of the virus by testing and isolation of people who are infected,” says Sandra Ciesek, director of the Geothe University Frankfurt’s Institute of Medical Virology in Germany. In mid-February, she was among the first to report that people with no symptoms could spread the virus. Since then, Ciesek has been working on a pooled testing technique to identify asymptomatic carriers. The approach “is trying to do more with the same number of tests,” says Tomer Hertz, a computational immunologist at Ben-Gurion University of the Negev in Israel, who is also developing a batch-testing strategy. There is a caveat, though: as the prevalence of the infection in a community goes up, the ability to save resources through group testing goes down.

Coronavirus Test Shortages Trigger a New Strategy: Group Screening, Marla Broadfoot, Scientific American

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Dilemma...

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Green Book Blog: The Technology Dilemma, Zoë Dowling

 

Topics: Biology, Chemistry, COVID-19, Nanotechnology, Physics, Research, STEM


As the coronavirus outbreak roils university campuses across the world, early-career scientists are facing several dilemmas. Many are worrying about the survival of cell cultures, laboratory animals, and other projects critical to their career success. And some are reporting feeling unwelcome pressure to report to their laboratories—even if they don’t think it’s a good idea, given that any gathering can increase the risk of spreading the virus.

It’s unclear exactly how common these concerns are, but social media posts reveal numerous graduate students expressing stress and frustration at requests to come to work. “Just emailed adviser to say I am not comfortable breaking self isolation to come to lab this week. They emailed … saying I have to come in. What do I do?” tweeted an anonymous Ph.D. student on 16 March who doesn’t have essential lab work scheduled. “My health & safety should NOT be subject to the whims of 1 person. It should NOT be this scary/hard to stand up for myself.”

Many universities, including Harvard, have moved to shut down all lab activities except for those that are deemed “essential,” such as maintaining costly cell lines, laboratory equipment, live animals, and in some cases, research relating to COVID-19. But others have yet to ban nonessential research entirely.

 

Amid coronavirus shutdowns, some grad students feel pressure to report to their labs
Michael Price, Science Magazine, AAAS

I feel their pain.


The Scientific Method is very simple in concept:

Problem research - This involves gathering data in the form of previous written papers, published and peer-reviewed; writing notes (for yourself), summaries and reviews.

Hypothesis - This is your question asked from all the research, discussion with your adviser, especially if it's a valid question to ask or research to pursue.

Test the hypothesis - Design of experiment (s) to verify the hypothesis.

Data analysis - Usually with a software package, and a lot of statistical analysis.

Conclusion - Does it support the hypothesis?

- If so, retest several times, to plot an R squared fit of the data, so predictions can be made.

- If not, form another hypothesis and start over.

Often, conclusions are written up for peer review to be considered for journal publication. No one ever gets in on first submission - get used to rejection. Conclusions will be challenged by subject matter experts that may suggest other factors to consider, or another way to phrase something. Eventually, you get published. You can then submit an abstract to present a poster and a talk at a national conference.

Meeting Cancellation

It is with deep regret that we are informing you of the cancellation of the 2020 APS March Meeting in Denver, Colorado. APS leadership has been monitoring the spread of the coronavirus disease (COVID-19) constantly. The decision to cancel was based on the latest scientific data being reported, and the fact that a large number of attendees at this meeting are coming from outside the US, including countries where the CDC upgraded its warning to level 3 as recently as Saturday, February 29.

 

APS Physics: March.APS/about/coronavirus/


Update on Coronavirus

The health and safety of MRS members, attendees, staff, and community are our top priority. For this reason, we are canceling the 2020 MRS Spring Meeting scheduled for April 13-17, 2020, in Phoenix.

With our volunteers, we are exploring options for rescheduling programming to an upcoming event. We will share more information as soon as it becomes available.

 

MRS: Materials Research Society/2020-Spring Meeting


Social distancing and "shelter-in-place" slows the scientific enterprise. Science is in-person and worked out with other humans in labs and libraries. However, I am in support of this action and reducing the impact on the healthcare industry that on normal days are dealing with broken bones, gunshot wounds; cancer and childbirth surgeries with anxious, expectant mothers.

The dilemma is the forces that would reject the science behind this pandemic (and most science in any endeavor), would have us all "go back to work" after two weeks. The curve we're trying to flatten could sharply spike. The infection rates would increase and otherwise healthy people would be stricken. Immunodeficient groups would start getting sick again ...dying again. Our infrastructure is not designed for that many sick or dead people. Science continues with our survival and societal stability.

The persons with the solutions might be chomping-at-the-bit at home for now. Survival insures science will continue ...someday.
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Social Distancing...

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Every square centimeter packed

 

Topics: Biology, Civics, Civil Rights, Existentialism


I shopped and bought the supplies you see above for the suggested "hunker down." It's the most I've ever purchased at one time in a grocery store. Missing from the pile of food, meat and cleaning supplies is hand sanitizer and toilet paper. Amazon is out, with delivery projections of off-brand toilet paper mid April, according to a college friend on lock down in California. Though I don't own a dog anymore, I observed dog food was missing from the shelves. The city is on limited hours from 10 am to 3 pm. The suggested crowd assemblies dwindled swiftly from 500 - 300 - 100 to 10 or less. There will likely be no spring commencement. Susan Rice was to be our keynote speaker, and I was going to attend to congratulate newly-minted Doctors of Philosophy.

My classes went online almost immediately through Blackboard. It was kind of cute to see my professors struggling and fully admitting they've never taught an online class before. The fact that they were lecturing was a departure from previous experiences, typically PowerPoint slides uploaded to Canvas (another college app), chapters read and a test proctored. That was my experience with it before. There's a video app: Zoom that I used to view a Ph.D. defense and a seminar on writing. My tiny house seems at comparison to my mobility before, smaller ...

I took a walk today in the neighborhood. Teleworking tends to drive one "stir crazy." I saw a family that lives across the street from me playing with her son in the street. She was accompanied by her brother, his girlfriend, her kids and their mother. The brother and his family had moved into the neighborhood. I said hello, mouthing a few brief remarks. I was friendly ...at a distance.

I continued walking.

A jogger passed by me on my right. A couple walked by on my left: I spoke briefly. I still walked.

A neighbor said "did anyone tell you you look like Charles Barkley?" I smiled: I've heard it before, and said "I wish I had his salary!" We laughed. I said it ...at a distance.

I continued walking.

A read on my phone about a few young spring breakers determined to party in Florida, full of the invulnerability of youth. They're not practicing social distancing, or good sense.

Italy passed a grim marker in the number of infected and deaths. I'm sure we're trying not to copy-exact this aspect of what was the Roman Empire in these modern times where the globe is no longer vast, and the oceans not the barriers they once were.

Columbus Day may not get as much attention as our other holidays, but scientists are still fascinated by what Christopher Columbus’ arrival meant for the “New World” and how it shaped where we are today.

“It was a culture clash, obviously,” said OMRF President Stephen Prescott, M.D. “But it also launched a clash of infectious diseases.”

Columbus and other visitors from Europe lived in agrarian societies and cities, he said. The viruses and bacteria that develop in farming and when large groups of people live together are different from those in a more nomadic society, like the American Indians.

Think about swine flu and bird flu, Prescott said. We’re always on the lookout for viruses that pass from humans to animals, mutate DNA, and then return to humans.

“Well, that didn’t just start last year. So long as humans have been raising livestock, we’ve been passing viruses back and forth,” he said. “When explorers from Europe reached the Americas, they brought livestock and they brought diseases and the result was devastating.”

In Hispaniola, Columbus’ first stop in the Americas, the native Taino population (an indigenous Arawak people) had no immunity to new infectious diseases, including smallpox, measles and influenza. There were an estimated 250,000 indigenous people in Hispaniola in 1492. By 1517, only 14,000 remained.

Oklahoma Medical Research Foundation: Columbus brought more than ships to the New World, October 10, 2013

Also:

Related link: Coronavirus statistics

Earth system impacts of the European arrival and Great Dying in the Americas after 1492
Alexander Koch, Chris Brierley, Mark M. Maslin, Simon L. Lewis
Quaternary Science Reviews
Volume 207, 1 March 2019, Pages 13-36


The conversation that hasn't been had: we're seeing not just the impact of a zoological virus from bat to human, we're seeing the impact of a globalization protocol that's been in place since 1492. The bats are in China, but bats are on every continent. The trade agreements we've negotiated for cheap labor also meant the ones in charge of the labor pool ignored (or, weren't pressed to follow) OSHA and safety regulations we take for granted. The "chickens [were eventually going to] come home to roost" because human society as far as temporal considerations is episodic. We think of the quarter, the end-of-year, the holiday push and financial goals higher than last years. We think of stock dividends and investor sentiments; use bailout money to buy back stocks and artificially pump up the value of their companies. This selloff on Wall Street has simply been an adjustment from the previous superfluous bullshit. My trip to Texas to see our granddaughter, relatives and friends; my wife's annual girlfriends' trip, our sons trip to Greensboro have all been put on hold indefinitely to flatten the curve.

I walked alone ...home, continuing social distancing.

 

Related link: Coronavirus statistics

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Crowd Sourcing...

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Image Source: Semantics Scholar link below

 

Topics: Biology, Existentialism, Politics


Note: As I'm getting my sea legs in online classes, the blog will post not at the normal times because these aren't normal times. My karate instructor from undergrad is a cancer survivor: his doctor has him in isolation as COVID-19 can be exacerbated by immunodeficient systems. In addition, his wife and daughter just came back from overseas and are in isolation. He has relatives visiting him, though.

A brief I wrote my first year of graduate school for a class called Nano Safety (excerpt):

From an article in Nature: Education, it posits that viruses are not ‘alive’ in a sense they don’t have metabolic processes, one of the four criteria for life (“organized, metabolism, genetic code, and reproduction”) as discussed in class, 24 August 2017. There are three possible mechanisms to origins. The Progressive Hypothesis: “bits and pieces” of a genome gained the ability to move in and out of cells (retroviruses like HIV given as an example). The Regressive Hypothesis: meaning the viruses evolved from some common ancestor to their current state. The Virus-First Hypothesis: that viruses existed before mortals as “self-replicating units.”

1. Where did viruses come from? Ed Rybicki, Virologist from the University of Cape Town in South Africa

2. The Origins of Viruses, By David R. Wessner, Ph.D. (Dept. of Biology, Davidson College) © 2010 Nature Education, Citation: Wessner, D. R. (2010) The Origins of Viruses. Nature Education 3(9):37

My wife and I suffer allergies during this time of year. Out of an abundance of caution, we attempted to have her tested for COVID-19. The doctor surmised she didn't have any symptoms of Coronavirus, but the inventory of test kits from the CDC is what really troubled me: ONE. Only if you meet the stringent requirement of damned-near death's door will anyone get the test. Then, the doctor will order another SINGULAR test.

Conclusion: Our numbers are being held down artificially.

We're sheltered in-place. I'm calling and texting friends to check on them.

North Carolina now has 63 confirmed cases of Coronavirus, but that's for those who met the criteria and GOT the singular test kit evaluation.

All of us are literally on our own.

In response to the COVID-19 pandemic, the Allen Institute for AI has partnered with leading research groups to prepare and distribute the COVID-19 Open Research Dataset (CORD-19), a free resource of over 29,000 scholarly articles, including over 13,000 with full text, about COVID-19 and the coronavirus family of viruses for use by the global research community.

This dataset is intended to mobilize researchers to apply recent advances in natural language processing to generate new insights in support of the fight against this infectious disease. The corpus will be updated weekly as new research is published in peer-reviewed publications and archival services like bioRxiv, medRxiv, and others.

 

Semantics Scholar: COVID-19 Open Research Dataset (CORD-19)

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Off World Concerns...

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NASA astronaut Chris Cassidy and Roscosmos cosmonauts Anatoly Ivanishin and Ivan Vagner are the next crewmembers scheduled to launch to the International Space Station.
(Image: © NASA)

 

Topics: Biology, NASA, International Space Station, Space Exploration


The procedure to ensure that astronauts don't bring an illness to the International Space Station is under evaluation as NASA enacts tactics to help slow the spread of the novel-coronavirus disease COVID-19.

Governments and agencies around the world have been enacting measures meant to contain the spread of the novel coronavirus; those measures include social distancing and quarantines for people who think they may have been exposed to the virus. But these tactics aren't new territory for NASA astronauts, who take such measures to prepare for close-quarter, secluded living that can last six months or longer.

 

With coronavirus spreading, NASA may tweak astronaut prelaunch quarantine plans
Doris Elin Urrutia, Space.com

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Proto Nanotechnologist...

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Professor George Washington Carver, Tuskegee University, History.com 


Topics: African Americans, Biology, Diversity, Diversity in Science, Nanotechnology


Part of being in nanotechnology is you get to exercise a bit of creativity and invention. Research is about looking into an area that people know something about, reading a LOT of papers and formulating your own ideas about an approach to a subject. You may either fail miserably at first, or successfully bring about something novel.

George Washington Carver I'm referring to as a proto nanotechnologist. Planting peanuts, soy and sweat potatoes replaced nitrogen other plants like cotton leached from the soil. Though this crop rotation method (introduced by Carver) gave the farmers high yields on the produce they were used to selling, it had the unintended consequence of giving them a surplus of produce for which, there had previously been no market. Carver would go on to invent 300 uses for the peanut, one of which, peanut butter he surprisingly DIDN'T, though I'm sure you've eaten unless you have allergies. If it weren't for him, the farmers in the south would have gone out of business due to a boll weevil infestation that decimated cotton throughout the south. It was a fortuitous confluence of events.

It is in this spirit and the month, I salute Professor George Washington Carver, and hopefully emulate him in my chosen field of making meaning of small things.

George Washington Carver was an agricultural scientist and inventor who developed hundreds of products using peanuts (though not peanut butter, as is often claimed), sweet potatoes and soybeans. Born an African American slave a year before slavery was outlawed, Carver left home at a young age to pursue education and would eventually earn a master’s degree in agricultural science from Iowa State University. He would go on to teach and conduct research at Tuskegee University for decades, and soon after his death his childhood home would be named a national monument — the first of its kind to honor an African American.

Born on a farm near Diamond, Missouri, the exact date of Carver’s birth is unknown, but it’s thought he was born in January or June of 1864.

Nine years prior, Moses Carver, a white farm owner, purchased George Carver’s mother Mary when she was 13 years old. The elder Carver reportedly was against slavery, but needed help with his 240-acre farm.

When Carver was an infant, he, his mother and his sister were kidnapped from the Carver farm by one of the bands of slave raiders that roamed Missouri during the Civil War era. They were sold in Kentucky.

Moses Carver hired a neighbor to retrieve them, but the neighbor only succeeded in finding George, whom he purchased by trading one of Moses’ finest horses. Carver grew up knowing little about his mother or his father, who had died in an accident before he was born.

 

George Washington Carver, Editors, History.com

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Xenobots...

 

Topics: Applied Physics, Biology, Nanotechnology, Robotics


A team of researchers have built what they claim to be the first living robots. The “xenobots,” they say, can move, pick up objects, and even heal themselves after being cut.

The team is hoping the biological machines could one day be used to clean up microplastics in the ocean or even deliver drugs inside the human body, The Guardian reports.

To build the robots, the team used living cells from frog embryos and assembled them into primitive beings.

“These are novel living machines,” research co-lead Joshua Bongard, robotics expert at the University of Vermont, said in a statement. “They’re neither a traditional robot nor a known species of animal. It’s a new class of artifact: a living, programmable organism.”

The millimeter-length robots were designed by a supercomputer running an “evolutionary algorithm” that tested thousands of 3D designs for rudimentary life forms inside a simulation. The scientists then built a handful of the designs, which were able to propel themselves forward or fulfill a basic task inside the simulation using tweezers and cauterizing tools.

The tiny robots had about a week to ten days of “power” courtesy of living heart muscle cells that were able to expand and contract on their own.

 

Scientists Build “First Living Robots” From Frog Stem Cells
Victor Tangermann, Futurism

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Protocells...

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This scanning electron microscope image was taken of artificial “protocells” created at Argonne’s Center for Nanoscale Materials, which have the ability to convert light to chemical energy through the use of a light-harvesting membrane. (Image by Argonne National Laboratory.)

 

Topics: Alternative Energy, Battery, Biology, Green Tech, Nanotechnology


By replicating biological machinery with non-biological components, scientists have found ways to create artificial cells that accomplish a key biological function of converting light into chemical energy.

In a study from the U.S. Department of Energy’s (DOE) Argonne National Laboratory, scientists created cell-like hollow capsule structures through the spontaneous self-assembly of hybrid gold-silver nanorods held together by weak interactions. By wrapping these capsules’ walls with a light-sensitive membrane protein called bacteriorhodopsin, the researchers were able to unidirectionally channel protons from the interior of the artificial cells to the external environment.

“Nature uses compartmentalization to accomplish biological functions because it brings in close vicinity the ingredients needed for chemical reactions,” said Argonne nanoscientist Elena Rozhkova, a corresponding author of the study. ​“Our goal was to replicate nature, yet use inanimate materials to probe how cells accomplish their biological tasks.”

 

Scientists harvest energy from light using bio-inspired artificial cells
Jared, Sagoff, Argonne National Laboratory

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