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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

Self-Tracking (The MIT Press Essential Knowledge series): Neff, Gina, Nafus, Dawn: 9780... - 0 views

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    "What happens when people turn their everyday experience into data: an introduction to the essential ideas and key challenges of self-tracking. People keep track. In the eighteenth century, Benjamin Franklin kept charts of time spent and virtues lived up to. Today, people use technology to self-track: hours slept, steps taken, calories consumed, medications administered. Ninety million wearable sensors were shipped in 2014 to help us gather data about our lives. This book examines how people record, analyze, and reflect on this data, looking at the tools they use and the communities they become part of. Gina Neff and Dawn Nafus describe what happens when people turn their everyday experience-in particular, health and wellness-related experience-into data, and offer an introduction to the essential ideas and key challenges of using these technologies. They consider self-tracking as a social and cultural phenomenon, describing not only the use of data as a kind of mirror of the self but also how this enables people to connect to, and learn from, others. Neff and Nafus consider what's at stake: who wants our data and why; the practices of serious self-tracking enthusiasts; the design of commercial self-tracking technology; and how self-tracking can fill gaps in the healthcare system. Today, no one can lead an entirely untracked life. Neff and Nafus show us how to use data in a way that empowers and educates."
Dennis OConnor

Love 2.0 - Online Tools - 0 views

  • Positivity Self Test
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    Recommended by Kabir: "In both Love 2.0 and her earlier book, Positivity, Dr. Barbara Fredrickson describes ground breaking research on our supreme emotion, love, as well as the hidden value of all positive emotions. She encourages readers to experiment with their own lives, finding ways to create more micro-moments of love and positivity that work for them. One way to begin is to keep track of your emotions on a regular basis. Dr. Fredrickson developed the Positivity Self Test featured in her research, her books, and on this website to help you assess your current positivity ratio and track changes in your ratio over time. Just like tracking calories or cash flows can heighten your awareness and in time help you meet your fitness or financial goals, tracking your positivity ratio can help you raise your ratio and build your best future. Results may vary. Best outcomes emerge from sincere and heartfelt efforts to raise your ratio coupled with honest reports of your emotion experiences. Read more about the Positivity Self Test or take the survey here."
Dennis OConnor

A third of people track their health or fitness. Who are they and why are they doing it? - 0 views

  • one in three people (33 percent) currently monitor or track their health or fitness via an online or mobile
  • international GfK survey
  • China is well in the lead
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  • Brazil and the USA come next
  • followed by Germany (28 percent) and France (26 percent).
  • To download full findings for each of the 16 countries, please visit www.gfk.com/global-studies/global-study-overview/
Dennis OConnor

Get Started - Quantified Self - 0 views

  • If your project requires a lot of work every day, you’re more likely to drop it before you learn anything useful.
  • Try a one number baseline: A baseline measurement can be as simple as a single number representing a single measurement.
  • collect and organize some of the most useful advice about self-tracking
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  • How do you get started with a self-tracking project?
  • The activities are: Questioning, Observing, Reasoning, and Consolidating Insight.
  • questions about a tool you’re currently using, try posting in the QS Forum.
  • Retrospective Annotation
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    "So: How do you get started with a self-tracking project? You can picture your project as involving four distinct activities. Although these activities blend into each other, they do each have their own particular flavor, and by outlining them separately we think we can give you a coherent and functional recipe. The activities are: Questioning, Observing, Reasoning, and Consolidating Insight."
Dennis OConnor

Predicting 'Long COVID Syndrome' with Help of a Smartphone App - NIH Director's Blog - 0 views

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    Recommended by Tyler Orion, Endorsed by DeAunne Denmark, MD, PhD :This is an example of the high quality and thoughtful study design needed to accurately and meaningfully interpret real-world tracking data. This prediction signal would not have been detected in the larger (inconsistently reporting) group, or in those who hadn't tracked enough before getting sick. Which relates to the importance of creating a baseline health timeline and consistently collecting robust, standardized pre-intervention contextual data. And another illustration re: why I keep circling back to these in all of our n-of-1 discussions :)
Dennis OConnor

The epic battle against coronavirus misinformation and conspiracy theories - 0 views

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    Recommended by Tyler Orion: "For researchers who track how information spreads, COVID-19 is an experimental subject like no other. "This is an opportunity to see how the whole world pays attention to a topic," says Renée diResta at the Stanford Internet Observatory in California. She and many others have been scrambling to track and analyse the disparate falsehoods floating around - both 'misinformation', which is wrong but not deliberately misleading, and 'disinformation', which refers to organized falsehoods that are intended to deceive. "
Dennis OConnor

Detect - App Scripps Research - 0 views

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    Download the Mydatahelps app -- "When your heart beats faster than usual, it can mean that you're coming down with a cold, flu, coronavirus, or other viral infection. That's the conclusion of recent medical research. So wearable devices that measure your resting heart rate-made by Apple, Fitbit, Garmin, and others-might help scientists spot viral outbreaks, and also give you more insight into your own health. At Scripps Research, we've designed DETECT (Digital Engagement & Tracking for Early Control & Treatment), a study that will monitor your heart rate and allow you to record symptoms like fever or coughing."
Dennis OConnor

The Challenge of Tracking COVID-19's Stealthy Spread - NIH Director's Blog - 0 views

  • The first thing that testing may help us do is to identify those SARS-CoV-2-infected individuals who have no symptoms, but who are still capable of transmitting the virus.
  • The second way we can use testing is to identify individuals who’ve already been infected with SARS-CoV-2, but who didn’t get seriously ill and can no longer transmit the virus to others.
Dennis OConnor

In the coronavirus pandemic, we're making decisions without reliable data - 4 views

  • A fiasco in the making? As the coronavirus pandemic takes hold, we are making decisions without reliable data
  • This evidence fiasco creates tremendous uncertainty about the risk of dying from Covid-19.
  • As most health systems have limited testing capacity, selection bias may even worsen in the near future.
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  • The one situation where an entire, closed population was tested was the Diamond Princess cruise ship and its quarantine passengers. The case fatality rate there was 1.0%, but this was a largely elderly population, in which the death rate from Covid-19 is much higher.
  • Projecting the Diamond Princess mortality rate onto the age structure of the U.S. population, the death rate among people infected with Covid-19 would be 0.125%. But since this estimate is based on extremely thin data — there were just seven deaths among the 700 infected passengers and crew — the real death rate could stretch from five times lower (0.025%) to five times higher (0.625%).
  • Although successful surveillance systems have long existed for influenza, the disease is confirmed by a laboratory in a tiny minority of cases.
  • Some worry that the 68 deaths from Covid-19 in the U.S. as of March 1610 will increase exponentially to 680, 6,800, 68,000, 680,000 … along with similar catastrophic patterns around the globe. Is that a realistic scenario, or bad science fiction? How can we tell at what point such a curve might stop?
  • In the absence of data, prepare-for-the-worst reasoning leads to extreme measures of social distancing and lockdowns.
  • This has been the perspective behind the different stance of the United Kingdom keeping schools open12, at least until as I write this. In the absence of data on the real course of the epidemic, we don’t know whether this perspective was brilliant or catastrophic.
  • One of the bottom lines is that we don’t know how long social distancing measures and lockdowns can be maintained without major consequences to the economy, society, and mental health.
  • At a minimum, we need unbiased prevalence and incidence data for the evolving infectious load to guide decision-making.
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    Dr. Michael Kurisu D.O. "My take is this article is written by a very credible source. John P.A. Ioannidis is from Stanford and great resource. Makes argument that we are basing a LOT of our decisions on faulty or NO data ! Its fascinating to me that there has been less than 10,000 deaths globally and we have had SO MUCH DISRUPTION in the economy. I definitely feel we should be tracking the amount of deaths that are going to occur from people that will be pushed into poverty as well as the number of people being denied access to medical care right now. Yes… with COVID19, it CAN get much worse…. But maybe not… we don't know yet. This article actually increased my morale and put me on track to help GET MORE DATA. Then we can make informed decisions. And then TRACK ALL THE DATA moving forward.
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    DeAunne Denmark, MD, PhD, "Excellent piece spelling out the pervasive and critical issues due to abysmal lack/tardiness in US testing, especially of large populations where initial outbreaks occurred, for those both visibly sick and not. And most importantly, healthcare workers. We cannot even begin to estimate CFR, much less develop reliable projection models, without valid data on everybody who is carrying. "The most valuable piece of information for answering those questions would be to know the current prevalence of the infection in a random sample of a population and to repeat this exercise at regular time intervals to estimate the incidence of new infections."
Dennis OConnor

http://jacobsschool.ucsd.edu/faculty/faculty_bios/findprofile.sfe?fmp_recid=360 - 0 views

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    Jurgen P. Schulze "Dr. Schulze's research focus is on making interactive 3D visualization systems easier to use. This includes both the visual display of the data, and input paradigms. Dr. Schulze uses high-end clustered graphics systems, such as virtual reality CAVEs to immerse the user in the data, and he uses 3D tracked input devices and more recently smart phones and tablets to interact with the virtual reality system. Dr. Schulze is the director of the Immersive Visualization Laboratory (IVL) at UC San Diego's Qualcomm Institute, the San Diego division of Calit2. In the CSE Department, Dr. Schulze teaches CSE 167 (Introduction to Computer Graphics) and CSE 165 (3D User Interfaces) and runs independent study projects in his laboratory at the Qualcomm Institute."
Dennis OConnor

Heart rate variability: A new way to track well-being - Harvard Health Blog - 0 views

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    Oura ring's Moments feature measures HRV. This is how we measure wellbeing. Test and measurement of wellbeing opens the door for so many interesting self studies. This should be one of the experimental choices in our new online class.
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

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

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    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

Milli | Artificial Intelligence Powered Health Coach - 0 views

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    "Meet Milli A self-teaching personalized medical intelligence platform built from real-time analysis of millions of patient/doctor interactions. The Medical Intelligence Platform™ makes it easy to capture, aggregate, and analyze comprehensive patient data with human-augmented Artificial Intelligence. We provide doctors with suggestions for the likely underlying dysfunctions that lead to disease, recommendations for follow up tests, and predictions for which intervention will be most effective for each patient. Our Virtual Health Assistant then provides intervention support to the patient and tracks their adherence and medical outcomes. This closed-loop process enables the platform to systematically learn from every provider/patient medical encounter to learn how to better prevent and reverse disease."
Dennis OConnor

What is biohacking? The new "science" of optimizing your brain and body. - Vox - 0 views

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    "Biohacking - also known as DIY biology - is an extremely broad and amorphous term that can cover a huge range of activities, from performing science experiments on yeast or other organisms to tracking your own sleep and diet to changing your own biology by pumping a younger person's blood into your veins in the hope that it'll fight aging. "
Dennis OConnor

Testing ramps up in California - 0 views

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    Source: LA Times 4/8/2020 As of Tuesday, California said it had results for 143,172 tests - or 362 per 100,000 people. That's a sharp increase from two weeks ago when just 39 of every 100,000 residents had been tested. Yet for all its deep sources of innovation, the state is behind the national average of 596 tests per 100,000, according to the COVID Tracking Project. In New York, which has far more people hospitalized with severe symptoms, testing has reached 1,748 of every 100,000.
Dennis OConnor

Infographic Time: Age isn't Just a Number, it's Yours to Control! - Elite HRV - 1 views

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    Everyone ages at different rates. Our "true age" (also called "biological age") depends on how much inflammation we encounter in our lifestyle and environment, combining with our genetics. True age represents our capacity for resilience, in tolerating and recovering from these life stresses. By increasing this resilience, we could even get younger in true age! It requires frequent tracking of biomarkers like heart rate variability (HRV).
Dennis OConnor

One Year of the Begin Within Journal! - Begin Within Today - 0 views

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    Christina P. Kantzavelos: "I created this journal because it didn't exist. I was couch-bound due to #lymedisease and a plethora of other diagnoses and symptoms and needed a way to track my physical and mental symptoms, document my nutrition, meds/supplements, challenges, successes, while focusing on self-love, gratitude and visualizations. I needed a way to see the light at the end of the tunnel. "
Dennis OConnor

Building the case for actionable ethics in digital health research supported by artific... - 0 views

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    "Abstract The digital revolution is disrupting the ways in which health research is conducted, and subsequently, changing healthcare. Direct-to-consumer wellness products and mobile apps, pervasive sensor technologies and access to social network data offer exciting opportunities for researchers to passively observe and/or track patients 'in the wild' and 24/7. The volume of granular personal health data gathered using these technologies is unprecedented, and is increasingly leveraged to inform personalized health promotion and disease treatment interventions. The use of artificial intelligence in the health sector is also increasing. Although rich with potential, the digital health ecosystem presents new ethical challenges for those making decisions about the selection, testing, implementation and evaluation of technologies for use in healthcare. As the 'Wild West' of digital health research unfolds, it is important to recognize who is involved, and identify how each party can and should take responsibility to advance the ethical practices of this work. While not a comprehensive review, we describe the landscape, identify gaps to be addressed, and offer recommendations as to how stakeholders can and should take responsibility to advance socially responsible digital health research."
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