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Dennis OConnor

Don't "Flatten the Curve," stop it! - Joscha Bach - Medium - 1 views

  • What all these diagrams have in common:
  • They have no numbers on the axes.
  • They don’t give you an idea how many cases it takes to overwhelm the medical system, and over how many days the epidemic will play out.
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  • They suggest that currently, the medical system can deal with a large fraction (like maybe 2/3, 1/2 or 1/3) of the cases, but if we implement some mitigation measures, we can get the infections per day down to a level we can deal with.
  • They mean to tell you that we can get away without severe lockdowns as we are currently observing them in China and Italy.
  • nstead, we let the infection burn through the entire population, until we have herd immunity (at 40% to 70%), and just space out the infections over a longer timespan.
  • The Curve Is a Lie
  • suggestions are dangerously wrong, and if implemented, will lead to incredible suffering and hardship.
  • Let’s try to understand this by putting some numbers on the axes.
  • California has only 1.8.
  • The US has about 924,100 hospital beds (2.8 per 1000 people)
  • Germany have 8
  • South Korea has 12
  • Based on Chinese data, we can estimate that about 20% of COVID-19 cases are severe and require hospitalization
  • many severe cases will survive if they can be adequately provided for at home
  • by some estimates can be stretched to about a 100,000, and of which about 30,000 may be available
  • mportant is the number of ICU beds
  • oxygen, IVs and isolation
  • About 6% of all cases need a ventilator
  • if hospitals put all existing ventilators to use, we have 160,000 of them
  • CDC has a strategic stockpile of 8900 ventilators
  • number of ventilators as a proximate limit on the medical resources, it means we can take care of up to 170,000 critically ill patients at the same time.
  • Without containment, the virus becomes endemic
  • Let’s assume that 55% of the US population (the middle ground) get infected between March and December, and we are looking at 180 million people.
  • the point of my argument is not that we are doomed, or that 6% of our population has to die, but that we must understand that containment is unavoidable, and should not be postponed, because later containment is going to be less effective and more expensive, and leads to additional deaths.
  • About 20% will develop a severe case and need medical support to survive.
  • Severe cases tend to take about 3–6 weeks to recover
  • 6% may need intubation and/or ventilation
  • Once a person is on the ventilator, it often takes about 4 weeks for them to get out of intensive care again.
  • The “flattening the curve” idea suggests that if we wash our hands and stay at home while being sick aggressively enough, we won’t have to stop the virus from becoming endemic and infecting 40% to 70% of all people, but we can slow the spread of the infection so much that out medical system can deal with the case load. This is how our normally distributed curve looks like when it contains 10.8 million patients, of which no more than 170,000 are ill at the same time:
  • Dampening the infection rate of COVID-19 to a level that is compatible with our medical system means that we would have to spread the epidemic over more than a decade!
  • confident that we will have found effective treatments until the
  • reducing the infectivity of the new corona virus to a manageable level is simply not going to be possible by mitigation, it will require containment.
  • My back-of-the-envelope calculation is not a proper simulation, or a good model of what’s going on either. Don’t cite it as such!
  • Of the 180 million, 80% will be regarded as “mild” cases.
  • Containment works
  • China has demonstrated to us that containment works
  • lockdown of Wuhan did not lead to starvation or riots
  • made it possible to focus more medical resources on the region that needed it most
  • implemented effective containment measures as soon as the first cases emerged.
  • South Korea was tracking its first 30 cases very well, until patient 31 infected over 1000 others on a church congregation.
  • For some reason, Western countries refused to learn the lesson.
  • The US, UK and Germany are not yet at this point: they try to “flatten the curve” by implementing ineffective or half hearted measures that are only meant to slow down the spread of the disease
  • instead of containing it.
  • some countries will stomp out the virus and others will no
  • few months from now
  • almost all travel from red zones into green zones will come to a hal
  • world will turn into red zones and green zones
  • Flattening the curve is not an option for the United States, for the UK or Germany. Don’t tell your friends to flatten the curve. Let’s start containment and stop the curve.
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    "Flattening the curve is not an option for the United States, for the UK or Germany. Don't tell your friends to flatten the curve. Let's start containment and stop the curve." Strong article with data visualizations from a Phd working out of MIT/Harvard.
Dennis OConnor

MIT SF Grand Hack 2019 - MIT Hacking Medicine - 0 views

  • Interested in disrupting healthcare? Join MIT Hacking Medicine as we bring the MIT Grand Hack to San Francisco! This is the weekend to brainstorm and build innovative solutions with hundreds of like-minded engineers, clinicians, designers, developers and business people. Within our multi-theme event, there is sure to be a healthcare challenge for everyone! Interested in helping out? You can partner with us, become a sponsor, or sign up to be a mentor! Email sfgrandhack@mit.edu for more information!Twitter Hashtag: #SFGrandHack2019 Frequently Asked Questions (FAQs)
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    "With approximately 133M Americans (more than 40% of the US population) suffering from one or more chronic diseases, the healthcare community is looking for more effective and efficient ways to manage chronic diseases. Part of that pursuit is in finding sustainable ways to help patients better understand their conditions and manage their health by empowering patients, connecting them to information, care, and therapies in ways they want. Join fellow innovators to work on a challenging, multi-faceted, meaningful opportunity to advance clinical care, quality of life, and outcomes for nearly half the US. How can we improve patient literacy and clinical understanding? How do we help patients feel more in-control of their medical care? What can be done to help patients understand when and where they should seek care? These are just some of the pain points begging for thoughtful, tech-enabled solutions."
Dennis OConnor

Healthcare Text Analytics: Unlocking the Evidence from Free Text | Frontiers Research T... - 0 views

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    "About this Research Topic Healthcare narratives (such as clinical notes, discharge letters, nurse handover notes, imaging reports, patients posts on social media or feedback comments, etc.) have been used as a key communication stream that contains the majority of actionable and contextualised data, but which - despite being increasingly available in a digital form - is still not routinely analysed, and is rarely integrated with other healthcare data on a large-scale. There are many barriers and challenges in processing healthcare free text, including, for example, the variability and implicit nature of language expressions, and difficulties in sharing training and evaluation data. On the other hand, recent years have witnessed increasing needs and opportunities to process free text, with a number of success stories that have demonstrated the feasibility of using advanced Natural Language Processing to unlock evidence contained in free text to support clinical care, patient self-management, epidemiological research and audit."
Dennis OConnor

World Health Organization China Joint Mission on covid-19 final-report.pdf - 0 views

shared by Dennis OConnor on 17 Mar 20 - No Cached
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    Goal and Objectives The overall goal of the Joint Mission was to rapidly inform national (China) and international planning on next steps in the response to the ongoing outbreak of the novel coronavirus disease (COVID-191) and on next steps in readiness and preparedness for geographic areas not yet affected.
Dennis OConnor

Kimbal Musk's Farm of the Future (Yes, Elon's brother) - YouTube - 0 views

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    "The way we get our food in the United States is completely messed up. When you go to the grocery store, especially in a city, most of the fresh fruits and vegetables you see have been trucked in from somewhere else, losing crucial nutritional value at an environmental cost. This is a huge problem, but Elon Musk's brother has a solution...in the form of a shipping container"
Dennis OConnor

UCSF Emergency COVID-19 Early Detection Research SUPPORT REQUEST - 1 views

shared by Dennis OConnor on 24 Mar 20 - No Cached
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    Click to download the PDF. Oura's primary goal is to help UCSF engage and increase the number of users who have rings and are opting in to early detection efforts. Oura is offering rings at $250 for orders of 1000 rings supporting TemPredict. Immediate impact: Participants are presented every morning with daily personalized insights on heart rate, HRv, respiration, temperature, sleep staging, and activity to empower them to monitor their own health and change their behavior accordingly. This is especially important in medical personnel and high-risk patients. Future impact: UCSF will leverage Oura's backend data to build models that can aid in identifying symptom profiles, pinpointing at risk populations, predicting severity, and validating recovery, containment, and treatment efforts. The data gathered now may be our only chance to measure these changes so we can recognize them and deploy predictive algorithms to minimize the next wave of this outbreak, expected in Fall 2020. We ask all donors to go to OuraRing.com and buy rings for medical personnel so they can join this effort.
Dennis OConnor

How breathing in wildfire smoke affects the body - 0 views

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    "For the more than seven million people in California's Bay Area living through historic wildfires, it's been hard to breathe for the past month. For 29 days the region has been under a "Spare the Air" alert, which means inhaling outdoor air presents a health hazard. Air quality is even worse in Oregon and Washington, and by this morning smoke had stretched all the way to the East Coast and even to Europe. Wildfire smoke contains a variety of gases and particles from the materials that fuel the fire, including ozone, carbon monoxide, polycyclic aromatic compounds, nitrogen dioxide, and particulate matter-pollutants linked to respiratory and cardiovascular illnesses, according to a study in the Journal of the American Heart Association."
Dennis OConnor

MIPACT Research Tools - 0 views

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    "This app contains physiologic and activity data for nearly 7,000 MIPACT study participants from the University of Michigan. To protect patient anonymity, data will only be displayed when 10 or more study participants have the selected combination of attributes. Data is available from the first 90-days of study participation and may be updated at a later date. Visit our MIPACT study website for more information."
Dennis OConnor

Personal Science… by Gary Isaac Wolf in collaboration with Thomas Blomseth Ch... - 0 views

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    "Thank you for considering buying our book, Personal Science: Learning to Observe. The book presents a step-by-step approach to exploring your personal questions with empirical methods. It contains no advice whatsoever on what treatments or medicines or diets or vitamins or exercises are worth trying. Instead, it offers meta-advice; that is, advice on how to know if the things that you try actually work the way you expect, and advice about how to develop reasonable new ideas of things to try."
Dennis OConnor

Invasive Yet Inevitable? Privacy Normalization Trends in Biometric Technology - 0 views

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    Abstract As biometric technology relies on bodily, physical information, it is among the more intrusive technologies in the contemporary consumer market. Consumer products containing biometric technology are becoming more popular and normalized, yet little is known about public perceptions concerning its privacy implications, especially from the perspective of human agency. This study examines how people perceive biometric technologies in different societal contexts and via different agents in control. Our study revealed that, in large part, people's perceptions of biometric technology are context-dependent, based on who retrieves and who benefits from the information and the situation where the data are collected. Participants were much more comfortable with more intrusive biometric technology in airport security than in a grocery store, and if it was employed to improve their health. We conclude by considering the implications of the survey for new threats to personal privacy that arise out of emerging technologies. Keywords biometric, facial recognition, DNA identification, digital privacy, digital data sharing, emerging technology, surveillance technology, contextual integrity, situational privacy
Dennis OConnor

A unified genealogy of modern and ancient genomes - 0 views

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    "Genomics and human ancestral genealogy Hundreds of thousands of modern human genomes and thousands of ancient human genomes have been generated to date. However, different methods and data quality can make comparisons among them difficult. Furthermore, every human genome contains segments from ancestries of varying ages. Wohns et al. applied a tree recording method to ancient and modern human genomes to generate a unified human genealogy (see the Perspective by Rees and Andrés). This method allows for missing and erroneous data and uses ancient genomes to calibrate genomic coalescent times. This permits us to determine how our genomes have changed over time and between populations, informing upon the evolution of our species. -LMZ"
Dennis OConnor

Apple and Google have a clever way of encouraging people to install contact-tracing app... - 0 views

  • Apple and Google surprised us with an announcement that the companies are spinning up a system to enable widespread contact tracing in an effort to contain the COVID-19 pandemic.
  • The basic idea is that as jurisdictions flatten the curve of infection and begin to consider re-opening parts of society, they need to implement a comprehensive “test and trace” scheme.
  • First, the companies said that by phase two of their effort, when contact tracing is enabled at the level of the operating system, they will notify people who have opted in to their potential exposure to COVID-19 even if they have not downloaded the relevant app from their public health authority.
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  • Apple and Google said they recognized the importance of not allowing people to trigger alerts based on unverified claims of a COVID-19 infection. Instead, they said, people who are diagnosed will be given a one-time code by the public health agency, which the newly diagnosed will have to enter to trigger the alert.
  • Google said it would distribute the operating system update through Google Play services, a part of Android controlled by the company that allows it to reach the majority of active devices.
  • Singapore saw only 12 percent adoption of its national contact-tracing app. Putting notifications at the system level represents a major step forward for this effort, even if still requires people to opt in.
  • the companies promised to use the system only for contact tracing, and to dismantle the network when it becomes appropriate.
Dennis OConnor

Advice from Dr. Mimi Guarneri - Integrative Medicine - 1 views

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    "Thankfully, there are many things we can do as individuals and communities that may be helpful. It is important to remain calm and think clearly. Remember that our positive attitudes go a long way in protecting health, enriching our daily lives, and supporting the ones we love. Here is a list of things one can do at home to help in these uncertain times:"
Dennis OConnor

Substantial undocumented infection facilitates the rapid dissemination of novel coronav... - 0 views

  • AbstractEstimation of the prevalence and contagiousness of undocumented novel coronavirus (SARS-CoV2) infections is critical for understanding the overall prevalence and pandemic potential of this disease. Here we use observations of reported infection within China, in conjunction with mobility data, a networked dynamic metapopulation model and Bayesian inference, to infer critical epidemiological characteristics associated with SARS-CoV2, including the fraction of undocumented infections and their contagiousness. We estimate 86% of all infections were undocumented (95% CI: [82%–90%]) prior to 23 January 2020 travel restrictions. Per person, the transmission rate of undocumented infections was 55% of documented infections ([46%–62%]), yet, due to their greater numbers, undocumented infections were the infection source for 79% of documented cases. These findings explain the rapid geographic spread of SARS-CoV2 and indicate containment of this virus will be particularly challenging.
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    Recommended by Jessica Block
Dennis OConnor

What Went Wrong with Coronavirus Testing in the U.S. | The New Yorker - 0 views

  • n February 5th, sixteen days after a Seattle resident who had visited relatives in Wuhan, China, was diagnosed as having the first confirmed case of COVID-19 in the United States, the Centers for Disease Control, in Atlanta, began sending diagnostic tests to a network of about a hundred state, city, and county public-health laboratories⁠. Up to that point, all testing for COVID-19 in the U.S. had been done at the C.D.C.; of some five hundred suspected cases⁠ tested at the Centers, twelve had confirmed positive. The new test kits would allow about fifty thousand patients to be tested, and they would also make testing much faster, as patient specimens would no longer have to be sent to Atlanta to be evaluated.
  • Before a state or local lab could use the C.D.C.-developed tests on actual patients
  • verification
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  • larger number, about thirty-six of them, received inconclusive⁠ results from one of the reagents.
  • Another five,
  • had problems with two reagents
  • On February 8th
  • we’re looking at exponential growth, and we need to figure out how to meet an exponential demand.”
  • the verification problems were “part of the normal procedures⁠.” In the meantime, she said, until new reagents could be manufactured, all COVID-19 testing in the United States would continue to take place exclusively at the C.D.C⁠.
  • The public-health-laboratory network was never intended to provide widespread testing in the event of a pandemic.
  • the three-week delay caused by the C.D.C.’s failure to get working test kits into the hands of the public-health labs came at a crucial time.
  • The void created by the C.D.C.’s faulty tests made it impossible for public-health authorities to get an accurate picture of how far and how fast the disease was spreadin
  • In hotspots like Seattle, and probably elsewhere, COVID-19 spread undetected for several weeks, which in turn only multiplied the need for more tests.
  • The problem was that containment was not done very well.
  • e cascading effects that they’ve had on the country’s COVID-19 preparations suggest a much larger problem with the way the United States has structured its pandemic response.
  • Yet flexibility was not what Jerome and his lab found when they tried to get an E.U.A. for their COVID-19 test.
  • problem was exacerbated by a President who has simultaneously underplayed the severity of the outbreak and overpromised the means available to fight it
  • problems with COVID-19 testing in the United States have obscured
  • triumph of modern medical science
  • Chinese scientists uploaded a copy of the virus’s genome to an online repository⁠, and virologists around the world set to work to develop diagnostic tests for the new disease
  • January 21st, a team in Berlin, led by Christian Drosten, one of the scientists who discovered the original SARS virus, in 2003, submitted the first paper to describe a protocol for testing for SARS-CoV-2.
  • That protocol would form the basis for a test disseminated, early on, by the World Health Organization
  • That same day, Messonnier announced that the C.D.C. had finalized its own test⁠, which it used to confirm the first known case of COVID-19 in the U.S.
  • The U.W. virology lab
  • started, probably in earnest in mid-January, to prepare what we call a laboratory-developed test,⁠
  • It took a team at the lab, working under the direction of Alex Greninger, about two weeks to develop a working version
  • But, as soon as Alex Azar, the Secretary of Health and Human Services, declared a public-health emergency, on February 4th, a new regulatory regime took effect. From that point on, any lab that wanted to conduct its own tests for the new coronavirus would first need to secure something called an Emergency Use Authorization from the F.D.A.
  • This shift in the regulations sounds perverse, since it restricts the use of new tests at precisely the moment they’re most needed.
  • E.U.A. process is supremely flexible.
  • several labs reported their problems to the C.D.C. In a briefing a few days later,
  • hen there’s a big emergency and we feel like we should really do something, it gets hard. It’s a little frustrating. We’ve got a lot of scientists and doctors and laboratory personnel who are incredibly good at making assays. What we’re not so good at is figuring out all the forms and working with the bureaucracy of the federal government.”
  • At one point, he was very frustrated because he’d e-mailed them what we were doing so they could review it,”
  • Here we are in this SARS-CoV-2 crisis, and you have to send them something through the United States Postal Service. It’s just shocking.
  • Despite these difficulties, Jerome said, the F.D.A. ultimately proved responsive to the lab’s entreaties. “They had good and substantive feedback that made our testing better, and the response time was typically just a couple of days.”
  • believe it was, February 29th,” he said. “And then we got a specimen from one of the people who were the two original cases in Washington
  • The E.U.A. regulations, however, prohibited the lab from reporting the results to the doctors who had ordered the tests for their patients.
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    "Sharfstein, too, thinks that it's fair to criticize the federal government for not recognizing that its pandemic plans had a single point of failure. The C.D.C. quickly developed a working test, and it was understandable, at some level, that people at the Centers thought that fixing the faulty reagents for the public-health labs would be faster than shifting to an entirely different protocol. Nevertheless, Sharfstein said, "Why are we relying only on the C.D.C.? What the F.D.A. could have done, and eventually did do, is say, 'You can use other approaches.' " Even so, he said, "I don't think it's quite fair to totally blame the F.D.A. for this. The F.D.A. can design an approach to support the public-health strategy, but someone has to tell F.D.A. the public-health goal." The delay in clearly establishing those goals, he said, shows why the decision to shut down the N.S.C. directorate was so consequential. "People talk about, like, why does it matter that they closed the White House office on pandemic preparedness? This is one reason.""
Dennis OConnor

The proximal origin of SARS-CoV-2 | Nature Medicine - 1 views

  • Here we review what can be deduced about the origin of SARS-CoV-2 from comparative analysis of genomic data
  • Our analyses clearly show that SARS-CoV-2 is not a laboratory construct or a purposefully manipulated virus.
  • The receptor-binding domain (RBD) in the spike protein is the most variable part of the coronavirus genome1,2. Six RBD amino acids have been shown to be critical for binding to ACE2 receptors and for determining the host range of SARS-CoV-like viruses7.
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  • Theories of SARS-CoV-2 originsIt is improbable that SARS-CoV-2 emerged through laboratory manipulation of a related SARS-CoV-like coronavirus.
  • the genetic data irrefutably show that SARS-CoV-2 is not derived from any previously used virus backbone
  • we propose two scenarios that can plausibly explain the origin of SARS-CoV-2: (i) natural selection in an animal host before zoonotic transfer; and (ii) natural selection in humans following zoonotic transfer.
  • COVID-19 were linked to the Huanan market in Wuhan
  • it is likely that bats serve as reservoir hosts for its progenitor
  • Malayan pangolins (Manis javanica) illegally imported into Guangdong province contain coronaviruses similar to SARS-CoV-221
  • Although no animal coronavirus has been identified that is sufficiently similar to have served as the direct progenitor of SARS-CoV-2, the diversity of coronaviruses in bats and other species is massively undersampled
  • For a precursor virus to acquire both the polybasic cleavage site and mutations in the spike protein suitable for binding to human ACE2, an animal host would probably have to have a high population density (to allow natural selection to proceed efficiently) and an ACE2-encoding gene that is similar to the human ortholog
  • It is possible that a progenitor of SARS-CoV-2 jumped into humans, acquiring the genomic features described above through adaptation during undetected human-to-human transmission.
  • All SARS-CoV-2 genomes sequenced so
  • are thus derived from a common ancestor that had them too
  • Estimates of the timing of the most recent common ancestor of SARS-CoV-2 made with current sequence data point to emergence of the virus in late November 2019 to early December 201923,
  • compatible with the earliest retrospectively confirmed cases
  • Basic research involving passage of bat SARS-CoV-like coronaviruses in cell culture and/or animal models has been ongoing for many years in biosafety level 2 laboratories across the world27, and there are documented instances of laboratory escapes of SARS-CoV28. We must therefore examine the possibility of an inadvertent laboratory release of SARS-CoV-2.
  • The finding of SARS-CoV-like coronaviruses from pangolins with nearly identical RBDs, however, provides a much stronger and more parsimonious explanation of how SARS-CoV-2 acquired these via recombination or mutation1
  • it is reasonable to wonder why the origins of the pandemic matter
  • Detailed understanding of how an animal virus jumped species boundaries to infect humans so productively will help in the prevention of future zoonotic events.
  • More scientific data could swing the balance of evidence to favor one hypothesis over another.
Dennis OConnor

The Prime Cellular Targets for the Novel Coronavirus - NIH Director's Blog - 0 views

  • Posted on May 5th, 2020 by Dr. Francis Collins
  • it has been remarkable and gratifying to watch researchers from around the world pull together and share their time, expertise, and hard-earned data in the urgent quest to control this devastating virus.
  • a recent study that characterized the specific human cells that SARS-CoV-2 likely singles out for infection [1
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  • This work was driven by the mostly shuttered labs of Alex K. Shalek, Massachusetts Institute of Technology, Ragon Institute of MGH, MIT, and Harvard, and Broad Institute of MIT and Harvard, Cambridge; and Jose Ordovas-Montanes at Boston Children’s Hospital. In the end, it brought together (if only remotely) dozens of their colleagues in the Human Cell Atlas Lung Biological Network and others across the U.S., Europe, and South Africa.
  • The discovery suggests that SARS-CoV-2 and potentially other coronaviruses that rely on ACE2 may take advantage of the immune system’s natural defenses.
  • t’s clear that these new findings, from data that weren’t originally generated with COVID-19 in mind, contained several potentially important new leads. This is another demonstration of the value of basic science.
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    "Posted on May 5th, 2020 by Dr. Francis Collins"
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