Researchers around the world have continued breathing new life into a retracted study, which suggested that common antihypertensive medications were harmful in patients with COVID-19. From a report: Published online on May 1, 2020 in the New England Journal of Medicine, the study relied on Surgisphere data to claim an association between renin-angiotensin-aldosterone system (RAAS) inhibitor therapy and worse outcomes in hospitalized COVID-19 patients with cardiovascular disease. The journal retracted the paper due to concerns about fraudulent data on June 4, 2020 in a widely publicized move, but the study has continued to rack up citations -- totaling at least 652 as of May 31, 2021, reported Todd Lee, MD, MPH, of McGill University in Montreal, and colleagues.

Just 17.6% of verified citations acknowledged or noted that the paper was retracted, according to their research letter published in JAMA Internal Medicine. In May of this year alone -- 11 months after the article was retracted -- it was referenced 21 times. "Our findings challenge authors, peer reviewers, journal editors, and academic institutions to do a better job of addressing the broader issues of ongoing citations of retracted scientific studies and protecting the integrity of the medical literature," Lee's group urged. The hypothesis that angiotensin-converting enzyme (ACE) inhibitors and angiotensin-receptor blockers (ARBs) may be harmful in patients with COVID-19 has been floated since the early days of the pandemic, with the reasoning being that since the SARS-CoV-2 virus enters human cells through ACE2 receptors, upregulation of these receptors could put patients at risk.

At the start of the pandemic, remembers MIT Technology Review's senior editor for AI, the community "rushed to develop software that many believed would allow hospitals to diagnose or triage patients faster, bringing much-needed support to the front lines — in theory.

"In the end, many hundreds of predictive tools were developed. None of them made a real difference, and some were potentially harmful." That's the damning conclusion of multiple studies published in the last few months. In June, the Turing Institute, the UK's national center for data science and AI, put out a report summing up discussions at a series of workshops it held in late 2020. The clear consensus was that AI tools had made little, if any, impact in the fight against covid.

This echoes the results of two major studies that assessed hundreds of predictive tools developed last year. Laure Wynants, an epidemiologist at Maastricht University in the Netherlands who studies predictive tools, is lead author of one of them, a review in the British Medical Journal that is still being updated as new tools are released and existing ones tested. She and her colleagues have looked at 232 algorithms for diagnosing patients or predicting how sick those with the disease might get. They found that none of them were fit for clinical use. Just two have been singled out as being promising enough for future testing. "It's shocking," says Wynants. "I went into it with some worries, but this exceeded my fears."

Wynants's study is backed up by another large review carried out by Derek Driggs, a machine-learning researcher at the University of Cambridge, and his colleagues, and published in Nature Machine Intelligence. This team zoomed in on deep-learning models for diagnosing covid and predicting patient risk from medical images, such as chest x-rays and chest computer tomography (CT) scans. They looked at 415 published tools and, like Wynants and her colleagues, concluded that none were fit for clinical use. "This pandemic was a big test for AI and medicine," says Driggs, who is himself working on a machine-learning tool to help doctors during the pandemic. "It would have gone a long way to getting the public on our side," he says. "But I don't think we passed that test...."

If there's an upside, it is that the pandemic has made it clear to many researchers that the way AI tools are built needs to change. "The pandemic has put problems in the spotlight that we've been dragging along for some time," says Wynants.
The article suggests researchers collaborate on creating high-quality (and shared) data sets — possibly by creating a common data standard — and also disclose their ultimate models and training protocols for review and extension. "In a sense, this is an old problem with research. Academic researchers have few career incentives to share work or validate existing results.

"To address this issue, the World Health Organization is considering an emergency data-sharing contract that would kick in during international health crises."

Yasmeen Abutaleb, Carolyn Y. Johnson, and Joel Achenbach, reporting at Washington Post: The delta variant of the coronavirus appears to cause more severe illness than earlier variants and spreads as easily as chickenpox, according to an internal federal health document that argues officials must "acknowledge the war has changed." The document is an internal Centers for Disease Control and Prevention slide presentation, shared within the CDC and obtained by The Washington Post. It captures the struggle of the nation's top public health agency to persuade the public to embrace vaccination and prevention measures, including mask-wearing, as cases surge across the United States and new research suggests vaccinated people can spread the virus.

The document strikes an urgent note, revealing the agency knows it must revamp its public messaging to emphasize vaccination as the best defense against a variant so contagious that it acts almost like a different novel virus, leaping from target to target more swiftly than Ebola or the common cold. It cites a combination of recently obtained, still-unpublished data from outbreak investigations and outside studies showing that vaccinated individuals infected with delta may be able to transmit the virus as easily as those who are unvaccinated. Vaccinated people infected with delta have measurable viral loads similar to those who are unvaccinated and infected with the variant.

"I finished reading it significantly more concerned than when I began," Robert Wachter, chairman of the Department of Medicine at the University of California at San Francisco, wrote in an email. CDC scientists were so alarmed by the new research that the agency earlier this week significantly changed guidance for vaccinated people even before making new data public. The data and studies cited in the document played a key role in revamped recommendations that call for everyone -- vaccinated or not -- to wear masks indoors in public settings in certain circumstances, a federal health official said.

An anonymous reader quotes a report from ScienceAlert: [A] team of surgeons has successfully completed the first human implantation in the US of an artificial heart device called the 'Aeson', developed by French company CARMAT. The artificial heart has two ventricular chambers and four biological valves, just like the real organ, and is powered by an external device. Made from "biocompatible materials" including bovine tissue, the artificial heart uses a combination of sensors and algorithms to maintain its pace and keep blood circulating through the body. "We are encouraged that our patient is doing so well after the procedure," says cardiologist Carmelo Milano from the Duke University School of Medicine. "As we evaluate this device, we are both excited and hopeful that patients who otherwise have few to no options could have a lifeline."

The patient in question is 39-year-old Matthew Moore, from Shallotte in North Carolina. Moore was initially due to have heart bypass surgery, but as his condition deteriorated the medical staff started to run out of options; he became so ill that even a regular heart transplant was too risky. Fortunately, he was in the right place: the Aeson device is being tested at Duke University, pending approval from the US Food and Drug Administration (FDA). It's already been given the green light for use by regulators in Europe, after several years of tests in European patients, not all of which have been successful. The artificial heart has been developed specifically to help those whose hearts can no longer pump enough blood through both chambers. It replaces the entire natural heart, although it's not intended to be permanent -- it's designed to be a bridge towards a full heart transplant within six months or so.

CIA Director William Burns says he has redoubled the agency's efforts to uncover the cause of Havana syndrome -- the mysterious set of ailments that has afflicted more than 200 U.S. officials and family members around the world. NPR reports: That includes the assignment of a senior officer who once led the hunt for Osama bin Laden to lead the investigation and tripling the size of a medical team involved in the probe, Burns told NPR on Thursday in his first sit-down interview since being confirmed as the agency's chief in March. "I am absolutely determined -- and I've spent a great deal of time and energy on this in the four months that I've been CIA director -- to get to the bottom of the question of what and who caused this," Burns said. "We're no longer the only big kid on the geopolitical block, especially with the rise of China. And as you know very well, there's a revolution in technology which is transforming the way we live, work, compete and fight. And so, CIA, like everyone else in the U.S. government, has to take that into account," he said.

Under Burns' direction, the CIA has tripled the number of full-time medical personnel at the agency who are focused on Havana syndrome and has shortened the waiting period for afflicted personnel to be admitted to the Walter Reed National Military Medical Center. "I'm certainly persuaded that what our officers and some family members, as well as other U.S. government employees, have experienced is real, and it's serious," Burns said. The director says he is seriously considering the "very strong possibility" that the syndrome is the result of intentional actions, adding that there are a limited number of "potential suspects" with the capability to carry out an action so widely across the globe. A report from last December by the National Academies of Sciences, Engineering, and Medicine found that microwave radiation is the "most plausible" explanation for the symptoms.

To head the task force investigating the syndrome, Burns has appointed a veteran officer who helped lead the hunt for Osama bin Laden. The identity of that officer is still undercover, according to The Wall Street Journal. "We're throwing the very best we have at this issue, because it is not only a very serious issue for our colleagues, as it is for others across the U.S. government, but it's a profound obligation, I think, of any leader to take care of your people," Burns said. The syndrome first appeared in 2016 at the U.S. Embassy in Havana, where more than 40 diplomats complained of symptoms such as migraines, dizziness, and memory loss. Dozens more cases have been reported in the years since.

Last week, about two dozen U.S. intelligence officers, diplomats, and other government officials in Vienna have reported experiencing mysterious afflictions similar to the Havana Syndrome." The Biden administration is "vigorously investigating" the reports, but the causes of the syndrome still remain unclear.

Last year the artificial intelligence group DeepMind cracked a mystery that has flummoxed scientists for decades: stripping bare the structure of proteins, the building blocks of life. Now, having amassed a database of nearly all human protein structures, the company is making the resource available online free for researchers to use. From a report: The key to understanding our basic biological machinery is its architecture. The chains of amino acids that comprise proteins twist and turn to make the most confounding of 3D shapes. It is this elaborate form that explains protein function; from enzymes that are crucial to metabolism to antibodies that fight infectious attacks. Despite years of onerous and expensive lab work that began in the 1950s, scientists have only decoded the structure of a fraction of human proteins.

DeepMind's AI program, AlphaFold, has predicted the structure of nearly all 20,000 proteins expressed by humans. In an independent benchmark test that compared predictions to known structures, the system was able to predict the shape of a protein to a good standard 95% of time. DeepMind, which has partnered with the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI), hopes the database will help researchers to analyse how life works at an atomic scale by unpacking the apparatus that drives some diseases, make strides in the field of personalised medicine, create more nutritious crops and develop "green enzymes" that can break down plastic.

"The efficacy of a drug being promoted by rightwing figures worldwide for treating Covid-19 is in serious doubt," reports the Guardian, "after a major study suggesting the treatment is effective against the virus was withdrawn due to 'ethical concerns'." The preprint study on the efficacy and safety of ivermectin — a drug used against parasites such as worms and headlice — in treating Covid-19, led by Dr Ahmed Elgazzar from Benha University in Egypt, was published on the Research Square website in November. It claimed to be a randomised control trial, a type of study crucial in medicine because it is considered to provide the most reliable evidence on the effectiveness of interventions due to the minimal risk of confounding factors influencing the results...

A medical student in London, Jack Lawrence, was among the first to identify serious concerns about the paper, leading to the retraction... He found the introduction section of the paper appeared to have been almost entirely plagiarised. It appeared that the authors had run entire paragraphs from press releases and websites about ivermectin and Covid-19 through a thesaurus to change key words. "Humorously, this led to them changing 'severe acute respiratory syndrome' to 'extreme intense respiratory syndrome' on one occasion," Lawrence said.

The data also looked suspicious to Lawrence... "In their paper, the authors claim that four out of 100 patients died in their standard treatment group for mild and moderate Covid-19," Lawrence said. "According to the original data, the number was 0, the same as the ivermectin treatment group. In their ivermectin treatment group for severe Covid-19, the authors claim two patients died, but the number in their raw data is four..." Lawrence contacted an Australian chronic disease epidemiologist from the University of Wollongong, Gideon Meyerowitz-Katz, and a data analyst affiliated with Linnaeus University in Sweden who reviews scientific papers for errors, Nick Brown, for help analysing the data and study results more thoroughly... "The main error is that at least 79 of the patient records are obvious clones of other records," Brown told the Guardian. "It's certainly the hardest to explain away as innocent error, especially since the clones aren't even pure copies. There are signs that they have tried to change one or two fields to make them look more natural..."

Meyerowitz-Katz told the Guardian that "this is one of the biggest ivermectin studies out there", and it appeared to him the data was "just totally faked".
Meta-analyses incorporating the "just totally faked" data were then published in Oxford Academic's Open Forum Infectious Diseases and in the American Journal of Therapeutics.

Meanwhile, the Guardian also notes a new (and peer-reviewed) paper that was just published last month in the journal Clinical Infectious Diseases. Its finding? Iermectin is "not a viable option to treat COVID-19 patients".

sciencehabit shares a report from Science Magazine: A man unable to speak after a stroke has produced sentences through a system that reads electrical signals from speech production areas of his brain, researchers report this week. The approach has previously been used in non-disabled volunteers to reconstruct spoken or imagined sentences, but this is the first demonstration of its potential in the type of patient it's intended to help. The participant had a stroke more than 10 years ago that left him with anarthria -- an inability to control the muscles involved in speech. Researchers used a computational model known as a deep-learning algorithm to interpret patterns of brain activity in the sensorimotor cortex, a brain region involved in producing speech, and 'decoded' sentences he attempted to read aloud.

In the new study, [the researchers] temporarily removed a portion of the participant's skull and laid a thin sheet of electrodes smaller than a credit card directly over his sensorimotor cortex. To "train" a computer algorithm to associate brain activity patterns with the onset of speech and with particular words, the team needed reliable information about what the man intended to say and when. So the researchers repeatedly presented one of 50 words on a screen and asked the man to attempt to say it on cue. Once the algorithm was trained with data from the individual word task, the man tried to read sentences built from the same set of 50 words, such as "Bring my glasses, please." To improve the algorithm's guesses, the researchers added a processing component called a natural language model, which uses common word sequences to predict the likely next word in a sentence. With that approach, the system only got about 25% of the words in a sentence wrong, they report today in The New England Journal of Medicine. With the new approach, the man could produce sentences at a rate of up to 18 words per minute.

The University of Oxford this week started vaccinations of a novel HIV vaccine candidate as part of a Phase I clinical trial in the UK. From a report: The goal of the trial, known as HIV-CORE 0052, is to evaluate the safety, tolerability, and immunogenicity of the HIVconsvX vaccine -- a mosaic vaccine targeting a broad range of HIV-1 variants, making it potentially applicable for HIV strains in any geographical region. Thirteen healthy, HIV-negative adults, aged 18-65 and who are considered not to be at high risk of infection, will initially receive one dose of the vaccine followed by a further booster dose at four weeks. The trial is part of the European Aids Vaccine Initiative (EAVI2020), an internationally collaborative research project funded by the European Commission under Horizon 2020 health programme for research and innovation.

Professor Tomas Hanke, Professor of Vaccine Immunology at the Jenner Institute, University of Oxford, and lead researcher on the trial, said: 'An effective HIV vaccine has been elusive for 40 years. This trial is the first in a series of evaluations of this novel vaccine strategy in both HIV-negative individuals for prevention and in people living with HIV for cure.' While most HIV vaccine candidates work by inducing antibodies generated by B-cells, HIVconsvX induces the immune system's potent, pathogen obliterating T cells, targeting them to highly conserved and therefore vulnerable regions of HIV -- an "Achilles heel" common to most HIV variants.

Most people in the poorest countries will need to wait another two years before they are vaccinated against COVID-19, researchers have told Nature. From a report: Around 11 billion doses are needed to fully vaccinate 70% of the world's population against COVID-19. As of 4 July, 3.2 billion doses had been administered. At the current vaccination rate, this will increase to around six billion doses by the end of the year, researchers from the International Monetary Fund, based in Washington DC, project. But so far, more than 80% of the doses have gone to people in high-income and upper-middle-income countries. Only 1% of people in low-income countries have been given at least one dose, according to the website Our World in Data.

Last month, the leaders of the G7 group of wealthy nations pledged extra doses for low- and middle-income countries (LMICs) by the end of 2022, at a summit in Cornwall, UK. The centrepiece was a promise from US President Joe Biden to donate 500 million doses of the vaccine made by pharmaceutical company Pfizer of New York City and biotechnology company BioNTech in Mainz, Germany. This is in addition to 87.5 million previously pledged. The United Kingdom pledged 100 million, and France, Germany and Japan have pledged around 30 million each.

The highly contagious Delta variant is on the rise, and countries that hoped they had seen the worst of Covid-19 are being battered again. From a report: The nightmare is returning. In Indonesia, grave diggers are working into the night, as oxygen and vaccines are in short supply. In Europe, countries are slamming their doors shut once again, with quarantines and travel bans. In Bangladesh, urban garment workers fleeing an impending lockdown are almost assuredly seeding another coronavirus surge in their impoverished home villages. And in countries like South Korea and Israel that seemed to have largely vanquished the virus, new clusters of disease have proliferated. Chinese health officials announced on Monday that they would build a giant quarantine center with up to 5,000 rooms to hold international travelers. Australia has ordered millions to stay at home.

A year and a half since it began racing across the globe with exponential efficiency, the pandemic is on the rise again in vast stretches of the world, driven largely by the new variants, particularly the highly contagious Delta variant first identified in India. From Africa to Asia, countries are suffering from record Covid-19 caseloads and deaths, even as wealthier nations with high vaccination rates have let their guard down, dispensing with mask mandates and reveling in life edging back toward normalcy. Scientists believe the Delta variant may be twice as transmissible as the original coronavirus, and its potential to infect some partially vaccinated people has alarmed public health officials.

A mix-and-match approach to Covid vaccines -- using different brands of jab for first and second doses -- gives good protection against the pandemic virus, a UK study has found. From a report: The Com-Cov trial looked at the efficacy of either two doses of Pfizer, two of AstraZeneca, or one of them followed by the other. All combinations worked well, priming the immune system. This knowledge could offer flexibility for vaccine rollout, say experts. The trial results also hint that people who have already received two doses of AstraZeneca vaccine could have a stronger immune response if they were given a different jab as a booster if recommended in the autumn. The UK's deputy chief medical officer, Prof Jonathan Van-Tam, said there was no reason to change the current successful same dose vaccine schedules in the UK, however, given vaccines were in good supply and saving lives. But he says it might be something to look at in the future: "Mixing doses could provide us with even greater flexibility for a booster programme, while also supporting countries who have further to go with their vaccine rollouts, and who may be experiencing supply difficulties."

University of Oxford scientists are trialing giving Ivermectin to people with Covid symptoms to see if it can keep them out of hospital. The BBC reports: The Principle study will compare those given the drug to patients receiving the usual NHS care. The drug has become controversial after being promoted for use across Latin America and in South Africa, despite being so far unproven. Previous studies of Ivermectin have generally been small or low quality. Most commonly used to treat parasitic infections such as river blindness, spread by flies, Ivermectin has also been shown to kill viruses in petri dishes in the lab -- although, at much higher doses than would usually be prescribed to people.

Dr Aurora Baluja, an anaesthesiologist and critical care doctor, said Ivermectin was often being given in parts of the world where there are high incidences of parasitic infections. Covid patients who are also fighting a parasitic disease at the same time would be likely to fare worse and that might explains some of its seemingly positive effect. Though there have been some early "promising" results from small and observational studies, Principle joint chief investigator Prof Richard Hobbs said it would be "premature" to recommend Ivermectin for Covid. [...] The Oxford team said they had selected Ivermectin to be included in the trial because it was "readily available globally" and known to be relatively safe (although, like most things, it can be toxic at very high doses). People aged 18-64 with an underlying health condition or experiencing breathlessness, and anyone aged 65 or over, can sign up to the Principle study within 14 days of having Covid symptoms or receiving a positive test. "All in all, though, the most compelling reports of ivermectin's effects seem to come from the smallest and least controlled samples (all the way down to anecdotal results) while the larger and more well-controlled trials tend to produce equivocal evidence at best," writes Derek Lowe, a medical chemist working in the pharmaceutical industry. "My current opinion is pretty much exactly that of the WHO guidance: I do not think that the current evidence is strong enough to say that ivermectin is a useful therapy for coronavirus patients. I know that there are quite a few studies out there in the literature, but they suffer from various combinations of small sample size, poor trial design, not enough data reported, and (in many cases) inconclusive statistics."

Should people on their deathbeds be allowed to try anything to save themselves? Should the entire world be allowed to practice self-care on a grand scale? These are some of the questions American author, journalist, and podcaster Matt Taibbi poses in an article via Substack. He argues that ivermectin "has become hostage to a larger global fight between populists and anti-populists."

UPDATE (2/18/2021): CNN reports "The antiparasitic drug ivermectin doesn't prevent severe disease from Covid-19 any more effectively than symptom management and close observation by medical professionals, according to a study published Friday in the journal JAMA Internal Medicine." In fact, slightly more patients in the ivermectin group went on to need extra oxygen compared with those who took a placebo, though the difference was not statistically significant.... [T]hey also looked at whether patients needed to be hospitalized, had to go on a ventilator, needed intensive care or died from their infections. There was no meaningful difference in outcomes between the group that took ivermectin and those who got the placebo treatment.

It was a randomized-controlled trial, the gold standard of medical research, in which researchers test an intervention against a placebo....

In addition to the fact that ivermectin didn't work, people who took it had more side effects than those who didn't, and sometimes those side effects were severe, including heart attacks, anemia and diarrhea that led to shock.

A simple blood test that can detect more than 50 types of cancer before any clinical signs or symptoms of the disease emerge in a person is accurate enough to be rolled out as a screening test, according to scientists. The Guardian reports: The test, which is also being piloted by NHS England in the autumn, is aimed at people at higher risk of the disease including patients aged 50 or older. It is able to identify many types of the disease that are difficult to diagnose in the early stages such as head and neck, ovarian, pancreatic, esophageal and some blood cancers. Scientists said their findings, published in the journal Annals of Oncology, show that the test accurately detects cancer often before any signs or symptoms appear, while having a very low false positive rate.

The test, developed by US-based company Grail, looks for chemical changes in fragments of genetic code "cell-free DNA (cfDNA)" that leak from tumors into the bloodstream. The Guardian first reported on the test last year and how it had been developed using a machine learning algorithm a type of artificial intelligence. It works by examining the DNA that is shed by tumors and found circulating in the blood. More specifically, it focuses on chemical changes to this DNA, known as methylation patterns. Now the latest study has revealed the test has an impressively high level of accuracy. Scientists analyzed the performance of the test in 2,823 people with the disease and 1,254 people without. It correctly identified when cancer was present in 51.5% of cases, across all stages of the disease, and wrongly detected cancer in only 0.5% of cases.

In solid tumors that do not have any screening options "such as esophageal, liver and pancreatic cancers" the ability to generate a positive test result was twice as high (65.6%) as that for solid tumors that do have screening options such as breast, bowel, cervical and prostate cancers. Meanwhile, the overall ability to generate a positive test result in cancers of the blood, such as lymphoma and myeloma, was 55.1%. The test correctly also identified the tissue in which the cancer was located in the body in 88.7% of cases.

The coronavirus vaccines made by Pfizer-BioNTech and Moderna may have caused heart problems in more than 1,200 Americans, including about 500 who were younger than age 30, according to data reported on Wednesday by researchers at the Centers for Disease Control and Prevention. Still, the benefits of immunization greatly outweighed the risks, and advisers to the C.D.C. strongly recommended vaccination for all Americans 12 and older. The New York Times: The heart problems reported are myocarditis, an inflammation of the heart muscle; and pericarditis, inflammation of the lining around the heart. The risk is higher after the second dose of an mRNA vaccine than after the first, the researchers reported, and much higher in men than in women. But overall, the side effect is very uncommon -- just 12.6 cases per million second doses administered. The researchers estimated that out of a million second doses given to boys ages 12 to 17, the vaccines might cause a maximum of 70 myocarditis cases, but would prevent 5,700 infections, 215 hospitalizations and two deaths. Agency researchers presented the data to members of the Advisory Committee on Immunization Practices, which makes recommendations on vaccine use in the United States. (The scientists grouped pericarditis with myocarditis for reporting purposes.) Most cases were mild, with symptoms like fatigue, chest pain and disturbances in heart rhythm that quickly cleared up, the researchers said. Of the 484 cases reported in Americans under age 30, the C.D.C. has definitively linked 323 cases to vaccination. The rest remain under investigation.

UPDATE (7/30): All the missing virus sequences have now been published, with their deletion being explained as just "an editorial oversight by a scientific journal," according to the New York Times.

In Slashdot's original report, an anonymous reader quoted another report from The New York Times: About a year ago, genetic sequences from more than 200 virus samples from early cases of Covid-19 in Wuhan disappeared from an online scientific database. Now, by rooting through files stored on Google Cloud, a researcher in Seattle reports that he has recovered 13 of those original sequences -- intriguing new information for discerning when and how the virus may have spilled over from a bat or another animal into humans. The new analysis, released on Tuesday, bolsters earlier suggestions that a variety of coronaviruses may have been circulating in Wuhan before the initial outbreaks linked to animal and seafood markets in December 2019. As the Biden administration investigates the contested origins of the virus, known as SARS-CoV-2, the study neither strengthens nor discounts the hypothesis that the pathogen leaked out of a famous Wuhan lab. But it does raise questions about why original sequences were deleted, and suggests that there may be more revelations to recover from the far corners of the internet.
UPDATE (6/25): The Washington Post notes the data wasn't exactly suppressed. "Processed forms of the same data were included in a preprint paper from Chinese scientists posted in March 2020 and, after peer review, published that June in the journal Small." And in addition: The NIH released a statement Wednesday saying that a researcher who originally published the genetic sequences asked for them to be removed from the NIH database so that they could be included in a different database. The agency said it is standard practice to remove data if requested to do so...

Bloom's paper acknowledges that there are benign reasons why researchers might want to delete data from a public database. The data cited by Bloom are not alone in being removed by the NIH during the pandemic. The agency, in response to an inquiry from The Post, said the National Library of Medicine has so far identified eight instances since the start of the pandemic when researchers had withdrawn submissions to the library.

"This one from China and the rest from submitters predominantly in the U.S.," the NIH said in its response. "All of those followed standard operating procedures."
The New York Times writes: The genetic sequences of viral samples hold crucial clues about how SARS-CoV-2 shifted to our species from another animal, most likely a bat. Most precious of all are sequences from early in the pandemic, because they take scientists closer to the original spillover event. As [Jesse Bloom, a virologist at the Fred Hutchinson Cancer Research Center who wrote the new report] was reviewing what genetic data had been published by various research groups, he came across a March 2020 study with a spreadsheet that included information on 241 genetic sequences collected by scientists at Wuhan University. The spreadsheet indicated that the scientists had uploaded the sequences to an online database called the Sequence Read Archive, managed by the U.S. government's National Library of Medicine. But when Dr. Bloom looked for the Wuhan sequences in the database earlier this month, his only result was "no item found." Puzzled, he went back to the spreadsheet for any further clues. It indicated that the 241 sequences had been collected by a scientist named Aisi Fu at Renmin Hospital in Wuhan. Searching medical literature, Dr. Bloom eventually found another study posted online in March 2020 by Dr. Fu and colleagues, describing a new experimental test for SARS-CoV-2. The Chinese scientists published it in a scientific journal three months later. In that study, the scientists wrote that they had looked at 45 samples from nasal swabs taken "from outpatients with suspected Covid-19 early in the epidemic." They then searched for a portion of SARS-CoV-2's genetic material in the swabs. The researchers did not publish the actual sequences of the genes they fished out of the samples. Instead, they only published some mutations in the viruses.

But a number of clues indicated to Dr. Bloom that the samples were the source of the 241 missing sequences. The papers included no explanation as to why the sequences had been uploaded to the Sequence Read Archive, only to disappear later. Perusing the archive, Dr. Bloom figured out that many of the sequences were stored as files on Google Cloud. Each sequence was contained in a file in the cloud, and the names of the files all shared the same basic format, he reported. Dr. Bloom swapped in the code for a missing sequence from Wuhan. Suddenly, he had the sequence. All told, he managed to recover 13 sequences from the cloud this way. With this new data, Dr. Bloom looked back once more at the early stages of the pandemic. He combined the 13 sequences with other published sequences of early coronaviruses, hoping to make progress on building the family tree of SARS-CoV-2. Working out all the steps by which SARS-CoV-2 evolved from a bat virus has been a challenge because scientists still have a limited number of samples to study. Some of the earliest samples come from the Huanan Seafood Wholesale Market in Wuhan, where an outbreak occurred in December 2019. But those market viruses actually have three extra mutations that are missing from SARS-CoV-2 samples collected weeks later. In other words, those later viruses look more like coronaviruses found in bats, supporting the idea that there was some early lineage of the virus that did not pass through the seafood market. Dr. Bloom found that the deleted sequences he recovered from the cloud also lack those extra mutations. "They're three steps more similar to the bat coronaviruses than the viruses from the Huanan fish market," Dr. Bloom said. This suggests, he said, that by the time SARS-CoV-2 reached the market, it had been circulating for awhile in Wuhan or beyond. The market viruses, he argued, aren't representative of full diversity of coronaviruses already loose in late 2019.
UPDATE (7/30): When republishing their sequences, the researchers indicated they actually came from January 30, 2020 (and not "late 2019").

Artificial intelligence is to be used to tackle the most deadly parasitic diseases in the developing world, tech company DeepMind has announced. The BBC reports: The London-based Alphabet-owned lab will work with the Drugs for Neglected Diseases initiative (DNDI) to treat Chagas disease and Leishmaniasis. Scientists spend years in laboratories mapping protein structures. But last year, DeepMind's AlphaFold program was able to achieve the same accuracy in a matter of days. Many diseases are linked to the roles of proteins in: catalysing chemical reactions (enzymes); fighting disease (antibodies); and acting as chemical messengers (hormones such as insulin). And knowing the 3D structure of a protein is important in developing treatments for, among others, cancer, dementia and infectious diseases.

Prof Dame Janet Thornton, of the European Bioinformatics Institute, told BBC News: "Most new drugs in recent years have been developed using protein-structural data as one part of the process. "There are, however, many other aspects which need to be taken into account, which, due to lack of data, may not be amenable to AI approaches." But the predictions would be "particularly valuable" for pathogens with unknown protein structures, including some neglected diseases. "Developing new AI approaches for designing such drugs is a new challenge but one to which the new AI techniques can be applied and this holds out great hope for the future," Dame Janet added.

Morgan Stanley plans to ban workers from its New York headquarters if they have not received a Covid-19 vaccine. The rule will apply to non-vaccinated guests and clients as well. From a report: According to a source close to the company, Morgan Stanley said in a memo to its employees in the New York metropolitan area that all staff working in buildings with a "large employee presence" are required to confirm their vaccination status by July 1. The source added that "vaccine attestation is on an honorary basis for employees, contingent workforce, clients and visitors." The company plans to expand the vaccination mandate to employees and guests in other Morgan Stanley locations in New York City and nearby Westchester starting July 12. "Operating within a fully vaccinated environment allows us to lift restrictions like the use of face coverings and the need to maintain physical distancing, returning to more normal office conditions," the source added.

Epic Systems' algorithm for identifying signs of sepsis, an often deadly complication from infections that can lead to organ failure, doesn't work as well as advertised, according to a new study published in JAMA Internal Medicine. The Verge reports: Epic says its alert system can correctly differentiate patients who do and don't have sepsis 76 percent of the time. The new study found it was only right 63 percent of the time. An Epic spokesperson disputed the findings in a statement to Stat News, saying that other research showed the algorithm was accurate. Sepsis is hard to spot early, but starting treatment as soon as possible can improve patients' chances of survival. The Epic system, and other automated warning tools like it, scan patient test results for signals that someone could be developing the condition. Around a quarter of US hospitals use Epic's electronic medical records, and hundreds of hospitals use its sepsis prediction tool, including the health center at the University of Michigan, where study author Karandeep Singh is an assistant professor.

The study examined data from nearly 40,000 hospitalizations at Michigan Medicine in 2018 and 2019. Patients developed sepsis in 2,552 of those hospitalizations. Epic's sepsis tool missed 1,709 of those cases, around two-thirds of which were still identified and treated quickly. It only identified 7 percent of sepsis cases that were missed by a physician. The analysis also found a high rate of false positives: when an alert went off for a patient, there was only a 12 percent chance that the patient actually would develop sepsis. Part of the problem, Singh told Stat News, seemed to be in the way the Epic algorithm was developed. It defined sepsis based on when a doctor would submit a bill for treatment, not necessarily when a patient first developed symptoms. That means it's catching cases where the doctor already thinks there's an issue. "It's essentially trying to predict what physicians are already doing," Singh said. It's also not the measure of sepsis that researchers would ordinarily use.

An anonymous reader quotes a report from The Guardian: From espresso to instant, coffee is part of the daily routine for millions. Now research suggests the brew could be linked to a lower chance of developing or dying from chronic liver disease. Chronic liver disease is a major health problem around the world. According to the British Liver Trust, liver disease is the third leading cause of premature death in the UK, with deaths having risen 400% since 1970. Writing in the journal BMC Public Health, Roderick and colleagues report how they analyzed data from 494,585 participants in the UK Biobank -- a project designed to help unpick the genetic and environmental factors associated with particular conditions. All participants were aged 40 to 69 when they signed up to the project, with 384,818 saying they were coffee drinkers at the outset compared with 109,767 who did not consume the beverage.

The team looked at the liver health of the participants over a median period of almost 11 years, finding 3,600 cases of chronic liver disease, with 301 deaths, and 1,839 cases of simple fatty liver disease. The analysis revealed that after taking into account factors such as body mass index, alcohol consumption, and smoking status, those who drank any amount of coffee, and of any sort, had a 20% lower risk of developing chronic liver disease or fatty liver disease (taken together) than those who did not consume the brew. The coffee drinkers also had a 49% lower risk of dying from chronic liver disease. The team said the magnitude of the effect increased with the amount of coffee consumed, up to about three to four cups a day, "beyond which further increases in consumption provided no additional benefit." A reduction in risk was also found when instant, decaffeinated and ground coffee were considered separately -- although the latter linked to the largest effect.