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Dennis OConnor

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

www.newyorker.com/...-coronavirus-testing-in-the-us

covid testing research

shared by Dennis OConnor on 18 Mar 20 - No Cached
  • 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
  • ...33 more annotations...
  • 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.
  • Dennis OConnor on 18 Mar 20
     
    "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

About Knight Lab - American Gut - 0 views

americangut.org/about

ecosystem

shared by Dennis OConnor on 29 May 18 - No Cached
  • The American Gut is based out of Rob Knight’s lab at the University of California, San Diego-meaning all samples provided by American Gut citizen science participants are processed by technicians working in the Knight lab.  The Knight lab is one of the largest microbiome research labs in the world, processing samples from hundreds of projects at a rate of ~100,000 per year. Notably, the protocols used by the lab to process these samples have been extensively tested and benchmarked and are freely available from the Earth Microbiome Project’s website.
Dennis OConnor

Knight Lab - 0 views

knightlab.ucsd.edu

ecosystem microbiome UCSD Apollo

shared by Dennis OConnor on 29 May 18 - No Cached
  • The Knight Lab uses and develops state-of-the-art computational and experimental techniques to ask fundamental questions about the evolution of the composition of biomolecules, genomes, and communities in different ecosystems, including the complex microbial ecosystems of the human body. We subscribe to an open-access scientific model, providing free, open-source software tools and making all protocols and data publicly available in order to increase general interest in and understanding of microbial ecology, and to further public involvement in scientific endeavors more generally.
  • Dennis OConnor on 29 May 18
     
    Rob Knight PHD, Embriette Hyde PHD, Sandrine Miller Montgomery PharmD PHD The Knight Lab uses and develops state-of-the-art computational and experimental techniques to ask fundamental questions about the evolution of the composition of biomolecules, genomes, and communities in different ecosystems, including the complex microbial ecosystems of the human body. We subscribe to an open-access scientific model, providing free, open-source software tools and making all protocols and data publicly available in order to increase general interest in and understanding of microbial ecology, and to further public involvement in scientific endeavors more generally.
Dennis OConnor

Mt. Sinai Lab100 - 0 views

www.lab100.org

mount-sinai integrative-spaces patient-centered research

shared by Dennis OConnor on 31 Oct 19 - No Cached
  • Dennis OConnor on 31 Oct 19
     
    Part clinic, part research lab, Lab100 uses precision diagnostics to empower patients and help scientists advance our understanding of human health.
Dennis OConnor

Mount Sinai Lab 100; reimagining how healthcare is delivered - 0 views

www.businessinsider.com/0s-clinic-of-the-future-2018-8

mount-sinai integrative-spaces patient-centered

shared by Dennis OConnor on 31 Oct 19 - No Cached
  • Dennis OConnor on 31 Oct 19
     
    Lab100 gives patients a comprehensive health risk assessment and biometric screening. The goal is to empower patients to track their health over time and to learn how their behavior and lifestyle are impacting their health in a very tangible way.
Dennis OConnor

First U.S. Company Announces an Upcoming Home COVID-19 Test | Time - 0 views

time.com/...home-covid-19-test-everlywell

covid research testing EverlyWell

shared by Dennis OConnor on 19 Mar 20 - No Cached
  • Food and Drug Administration allowed certified labs, including commercial lab testing companies, to develop and distribute COVID-19 tests on Feb. 29.
  • People can order the Everlywell COVID-19 test on the company’s website, after first answering questions about their basic health, symptoms and risk factors for the coronavirus disease. A doctor still needs to prescribe the test, so telemedicine doctors from PWNHealth, a national network of physicians who prescribe diagnostic tests, then reviews these answers to determine if a person qualifies for testing, based on criteria established by the Centers for Disease Control and Prevention.
  • Currently, because COVID-19 tests are not plentiful in the U.S., doctors are trying to rule out other respiratory diseases like flu first, and only ordering tests for people with symptoms who also have other risk factors for infection, such as being in close contact with others who have been diagnosed.
  • ...7 more annotations...
  • If the telemedicine doctor decides to prescribe an Everlywell COVID-19 test, the company says it will send the $135 test kit in two days (customers can pay $30 more to receive the kit overnight).
  • As with many of the commercially available tests, this one extracts SARS-CoV-2, the virus behind COVID-19, from the sample and then probes for specific genetic signatures of the virus.
  • If the test is positive, the company also provides a full telemedicine consultation with one of around 200 physicians that is included in the cost of the test.
  • Everlywell says it is ready to ship 30,000 COVID-19 tests, and plans to expand the number of labs processing the sample
  • kits will depend on the availability of swabs for collecting samples
  • global shortage of swabs for any lab performing the test.
  • We’re working hard to ramp up weekly capacity to test 250,000 Americans,” says Cheek
  • Dennis OConnor on 20 Mar 20
     
    DeAunne Denmark, M.D. Phd - I was just reading about this last night. Dr forum blowing up about it. It could be a gigantic win for EverlyWell (and at-home D-T-C Direct-to-Consumer) if they do it right. But *must* do it right, e.g. including transparency re: methods, interfacing with HCP/EMRs, etc. The big issue may be collection variability, not unlike the microbiome. Nasal swab not trivial, more talk now about collection variability possibly accounting for a large proportion of "negs" turning positive. Hate to see a lot of false confidence running around at large infecting others.
Dennis OConnor

Researchers Cast Doubt On Theory Of Coronavirus Lab Accident : Goats and Soda : NPR - 1 views

www.npr.org/...ry-of-coronavirus-lab-accident

covid research origins-covid-19

shared by Dennis OConnor on 24 Apr 20 - No Cached
  • April 23, 2020
  • Virus researchers say there is virtually no chance that the new coronavirus was released as result of a laboratory accident in China or anywhere else.
  • after corresponding with 10 leading scientists who collect samples of viruses from animals in the wild, study virus genomes and understand how lab accidents can happen, NPR found that an accidental release would have required a remarkable series of coincidences and deviations from well-established experimental protocols.
  • ...12 more annotations...
  • All of the evidence points to this not being a laboratory accident," says Jonna Mazet, a professor of epidemiology at the University of California, Davis and director of a global project to watch for emerging viruses called PREDICT.
  • all believe that the virus was transmitted between animals and humans in nature, as has happened in previous outbreaks — from Ebola to the Marburg virus — and with other known coronaviruses such as SARS and MERS.
  • Regardless, genetic analysis shows the virus began to spread sometime in the fall or winter of 2019, says Robert Garry, a microbiologist at Tulane University. Those same analyses refuted an earlier theory that the virus was genetically engineered in a laboratory.
  • the exact route from nature to people remains a mystery,
  • Rather than a laboratory misstep, researchers believe that this new coronavirus reached humans in the same way that other coronaviruses have: through "zoonotic spillover," or humans picking up pathogens from wildlife.
  • The CDC estimates that 6 out of 10 infectious diseases in people come from animals, including diseases caused by coronaviruses.
  • "As we change the landscape to suit our purposes, we come more and more into contact with viruses and other pathogens that we don't have much exposure to," says Dr. Brian Bird, associate director of the OneHealth Institute at UC Davis School of Veterinary Medicine and a former CDC scientist.
  • "Zoonotic transmission" or "zoonotic spillover" generally happens three ways: through excretion (feces that comes into contact with humans), slaughter (meat consumed by humans) and vector-borne (an animal biting a human). But even under these circumstances, the virus must then overcome barriers within the human body, defeating the immune system, to successfully replicate and transmit between humans themselves.
  • Despite the evidence, misinformation about the virus's origins continue to proliferate. For Daszak, who has worked on other outbreaks, the pattern is all too familiar: "Every time we get a new virus emerging, we have people that say, 'This could have come from a lab,' " he says.
  • "It's a real shame that the conspiracy theories can get to the level they've got with policymakers,"
  • The political heat has strained the very scientific collaborations meant to detect these viruses as they emerge, warns Jonna Mazet.
  • Daszak says the time for finger-pointing is over. "We have a bat virus in my neighborhood in New York killing people," he says. "Let's get real about this."
  • Dennis OConnor on 24 Apr 20
     
    "April 23, 2020"
Dennis OConnor

Home | The Hood-Price Lab for Systems Biomedicine - 0 views

hood-price.systemsbiology.org

Lee-Hood ecosystem

shared by Dennis OConnor on 16 Jun 18 - No Cached
  • Dennis OConnor on 16 Jun 18
     
    ""Systems biology and medicine - not only in the lab but in the everyday lives of people - challenges the imagination and will transform the 21st Century.""
Dennis OConnor

WIFIRE Lab - YouTube - 0 views

www.youtube.com/...UCrKsxI7TEp0KbD0D0iM5zSw

youtube data data visualization

shared by Dennis OConnor on 22 Jul 21 - No Cached
  • Dennis OConnor on 22 Jul 21
     
    Jessica Block's Lab - Subscribe to support the work.
Dennis OConnor

BJ Fogg | Behavior Design Lab - 1 views

behaviordesign.stanford.edu/...bj-fogg

BJFogg Behavior Design tiny-behavior

shared by Dennis OConnor on 04 Aug 21 - No Cached
  • Dennis OConnor on 04 Aug 21
     
    Recommended by Gina Soloperto. Dr. BJ Fogg founded the Behavior Design Lab at Stanford University, where he directs research and innovation. In addition, he teaches industry innovators how to use his models and methods in Behavior Design. The purpose of his research and teaching is to help millions of people improve their lives.
Dennis OConnor

Sharon Terry: Science didn't understand my kids' rare disease until I decided to study ... - 0 views

www.ted.com/...se_until_i_decided_to_study_it

shared by Dennis OConnor on 23 Jan 19 - No Cached
  • Dennis OConnor on 23 Jan 19
     
    "Meet Sharon Terry, a former college chaplain and stay-at-home mom who took the medical research world by storm when her two young children were diagnosed with a rare disease known as pseudoxanthoma elasticum (PXE). In this knockout talk, Terry explains how she and her husband became citizen scientists, working midnight shifts at the lab to find the gene behind PXE and establishing mandates that require researchers to share biological samples and work together."
Dennis OConnor

Galileo - Open Humans - 0 views

www.openhumans.org/...galileo

UCSD gut ecosystem galileo vineet

shared by Dennis OConnor on 06 Jun 18 - No Cached
  • Dennis OConnor on 06 Jun 18
     
    "Galileo is a website (designed by UC San Diego Design Lab) where people design and run their own experiments with their community. Anyone curious about their lifestyle and health can use this website; No prior knowledge is needed as the website guides people through the different steps of creating an experiment. After creating their experiment, people can it reviewed from two members who'll help them improve their experiment. Finally, people can invite others to participate in their experiment and begin it for a week when sufficient people join their experiment. By comparing their experiences an experiment, people provide researchers cues to build associations between lifestyle and health."
Dennis OConnor

Reverse Alzheimer's Disease (Current Trial) - 0 views

pmri.org/...zheimers-disease-current-trial

ornish robknight

shared by Dennis OConnor on 31 Aug 19 - No Cached
  • Dennis OConnor on 31 Aug 19
     
    "Can Lifestyle Changes Reverse Alzheimer's Disease? Dr. Dean Ornish, Dr. Bruce Miller, and Dr. Joel Kramer are directing the first randomized controlled trial to determine if the progression of early stage Alzheimer's disease may be reversed by a comprehensive lifestyle medicine program, without drugs, devices, or surgery. This lifestyle medicine program includes a whole foods low-fat, low-sugar plant-based diet;moderate exercise; stress management techniques including meditation; and psychosocial support." Tied into Rob Knight's lab
Dennis OConnor

The Design Lab - UC San Diego - 0 views

designlab.ucsd.edu

design-thinking ecosystem

shared by Dennis OConnor on 29 May 18 - No Cached
  • Dennis OConnor on 29 May 18
     
    he UC San Diego Design Lab works on major societal issues, such as large-scale education, automation, healthcare, visualization of complex phenomena and data, social interactions, citizen science, and the ethical issues that are of ever-increasing importance.
Dennis OConnor

Chasing My Cure: Dr. David Fajgenbaum Lessons from his Rare Disease and On Finding Cure... - 0 views

exponential.singularityu.org/...nd-on-finding-cures-for-others

storytelling research ecosystem self-study

shared by Dennis OConnor on 16 Mar 20 - No Cached
  • Dennis OConnor on 16 Mar 20
     
    "David Fajgenbaum, MD, MBA, MSc, is the co-founder and Executive Director of the Castleman Disease Collaborative Network (CDCN) and one of the youngest individuals to be appointed to the faculty at Penn Medicine, where he is an Assistant Professor of Medicine in Translational Medicine & Human Genetics, Founding Director of the Center for Study & Treatment of Castleman & inflammatory Lymphadenopathies (CSTL). An NIH-funded physician-scientist, he has dedicated his life to discovering new treatments and cures for deadly disorders like idiopathic multicentric Castleman disease (iMCD), which he was diagnosed with during medical school. As common as ALS and more deadly than lymphoma, iMCD involves the immune system attacking and shutting down the body's vital organs such as the liver, kidneys, bone marrow, and heart. After spending months hospitalized in critical condition, having his last rites read, and having four deadly relapses, he is now in his longest remission ever thanks to a treatment that he identified in the lab."
Dennis OConnor

Our Founders' Story | Scientific Learning - 0 views

www.scilearn.com/...ourfounders-story

reading

shared by Dennis OConnor on 23 Oct 19 - No Cached
  • Dennis OConnor on 23 Oct 19
     
    "The story of Scientific Learning begins with four research scientists: Michael Merzenich, William Jenkins, Paula Tallal, and Steven Miller. When the work of these four scientists intersected, their collaboration proved that the underlying cognitive processes that influence speech and language problems could be identified-and permanently improved. These findings led to the development of the Fast ForWord program, a groundbreaking computer-based reading intervention. The scientists then founded Scientific Learning to bring their program out of the lab and into the lives of struggling readers."
  • Dennis OConnor on 23 Oct 19
     
    Keywords: neuroscience reading
Dennis OConnor

precision medicine at stanford medicine x - 0 views

medicinex.stanford.edu/pmi

precision medicine ecosystem

shared by Dennis OConnor on 02 Jun 18 - No Cached
  • Dennis OConnor on 02 Jun 18
     
    "Medicine X is Stanford University's premier health care innovation program focusing on the intersection of emerging technologies and medicine. Our initiative is a catalyst for new ideas, and explores how we can work together to advance the practice of medicine, implement new approaches to healthcare such as precision medicine, and empower all stakeholders to be active participants in discussions about the future of health care. Under the direction of Dr. Larry Chu, Associate Professor of Anesthesia at Stanford School of Medicine, and guided by the Everyone Included™ framework for co-creation and leadership, Medicine X is a project of the Stanford AIM Lab and a growing international community."
Dennis OConnor

Doctors on the Frontlines of the Coronavirus Fight - The Atlantic - 0 views

www.theatlantic.com/...608509

covid research testing first-responders

shared by Dennis OConnor on 23 Mar 20 - No Cached
  • Yui had always counted herself lucky to be among a family of doctors. Now the family is facing the greatest challenge of their lives as they wrestle with the dilemma of caring for their patients even though this risks exposing their loved one
  • Will her family survive the crisis intact?
  • Doctors across America are facing similar predicaments, made all the more acute by the government’s failure to protect them—to warn the public, to provide tests, and to supply enough protective equipment.
  • ...13 more annotations...
  • When it comes to us being doctors, I worry about [family members] Stephanie and Alex and Jennifer and Pam—about their health, and about the eventual burnout due to everything that’s going on,”
  • As a primary-care physician, she’s the first point of contact with the medical system for many patients.
  • Pam recommended a hospital visit to be tested. “It was already too late for me and my family,” Pamela told me—she had been potentially exposed. Her patient got tested on March 12, and is still waiting for results. “My patient’s test was sent from Baltimore to a lab in Utah, then due to a reagent shortage [a substance needed to process the tests] sent from Utah to Arizona, Arizona back to a lab in North Carolina,” she said.
  • This is a mirror of the dysfunction and delays surrounding the country’s testing crisis, a major factor hamstringing the fight against the virus.
  • Meanwhile, she started feeling sick on Tuesday, and took the test herself. Self-quarantined at home, she thinks it’s only a matter of time, if she does have the virus, before she infects her two children—totally isolating from them would be all but impossible.
  • As a health-care provider, if I test positive, it has big implications for my office, my staff, and all the patients,”
  • Emergency-room doctors, he noted, are among those most at risk.
  • Her emergency room has been seeing more and more patients who have symptoms
  • She wears protective equipment but knows that the hospital could run out.
  • It’s not lost on Koo and her family that medical professionals worldwide have been dying fighting the coronavirus.
  • the main dilemma they’re grappling with is not so much getting sick themselves but spreading the virus to their families, their patients, and the public.
  • his might be the greatest fear of doctors across the country—that they’ll move from being part of the solution to part of the problem.
  • should. It weighs heavily on people.”Yui, for her part, told me she’d never let her fears over the virus stop her from doing her job.
  • Dennis OConnor on 23 Mar 20
     
    Dr. Michael Kurisu D.O.: Another article capturing the dialogue that i hear from a lot of my colleagues and others. We have doctors as well In my family : -My sister is Neuro ICU and director of stroke at Tri city hospital in Oceanside -Her husband is ER doc -My little sister is the PhD in sociology. (She specializes in education programs for the incarcerated and has interest on health access for prisons - which is a frightful place during this pandemic)
  • Dennis OConnor on 23 Mar 20
     
    We are in a war against this virus. First responders are the first line of defense. There is a lack of supplies and central leadership. However, there is no shortagage of courage. When you meet a first responder, say, "Thank you for your service."
Dennis OConnor

The Design Lab: Applying the Wisdom of the University to Societal Issues - 0 views

www.amacad.org/...dom-university-societal-issues

shared by Dennis OConnor on 30 May 19 - No Cached
  • Dennis OConnor on 30 May 19
     
    May 31, 2019 presentation Atkinson Hall, 5-8 pm
Dennis OConnor

Scientists Unlock 47 New Editable Genes After Purchasing CRISPR Expansion Pack - 0 views

www.theonion.com/nes-after-purchasin-1847764241

shared by Dennis OConnor on 01 Oct 21 - No Cached
  • Dennis OConnor on 01 Oct 21
     
    "BOSTON-Having exhausted the possibilities of the chromosome pairs that came preloaded on the original human genome, researchers at Harvard Medical School's Department of Genetics told reporters Wednesday they had unlocked 47 new editable genes following their purchase of a CRISPR expansion pack. "This add-on has a ton of incredible new genes, and we can't wait to start inserting them into our lab specimens," said Kevin Spiros, a professor of genetics, remarking that there was nothing more fun than having "some fresh strands of recombinant DNA to play around with." "
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