Skip to main content

Home/ PHE - Resources/ Group items tagged data

Rss Feed Group items tagged

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.
  • ...18 more annotations...
  • 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

Which Covid-19 Data Can You Trust? - 0 views

  • incomplete or incorrect data can also muddy the waters, obscuring important nuances within communities, ignoring important factors such as socioeconomic realities, and creating false senses of panic or safety, not to mention other harms such as needlessly exposing private information.
  • Right now, bad data could produce serious missteps with consequences for millions.
  • Whether you’re a CEO, a consultant, a policymaker, or just someone who is trying to make sense of what’s going on, it’s essential to be able to sort the good data from the misleading — or even misguided.
  • ...24 more annotations...
  • common red flags
  • Data products that are too broad, too specific, or lack context.
  • Public health practitioners and data privacy experts rely on proportionality
  • only use the data that you absolutely need for the intended purpose and no more.
  • Even data at an appropriate spatial resolution must be interpreted with caution — context is key.
  • Simply presenting them, or interpreting them without a proper contextual understanding, could inadvertently lead to imposing or relaxing restrictions on lives and livelihoods, based on incomplete information.
  • The technologies behind the data are unvetted or have limited utility.
  • Both producers and consumers of outputs from these apps must understand where these can fall short.
  • In the absence of a tightly coupled testing and treatment plan, however, these apps risk either providing false reassurance to communities where infectious but asymptomatic individuals can continue to spread disease, or requiring an unreasonably large number of people to quarantine.
  • Some contact-tracing apps follow black-box algorithms, which preclude the global community of scientists from refining them or adopting them elsewhere.
  • These non-transparent, un-validated interventions — which are now being rolled out (or rolled back) in countries such as China, India, Israel and Vietnam — are in direct contravention to the open cross-border collaboration that scientists have adopted to address the Covid-19 pandemic.
  • Models are produced and presented without appropriate expertise.
  • Epidemiological models that can help predict the burden and pattern of spread of Covid-19 rely on a number of parameters that are, as yet, wildly uncertain.
  • n the absence of reliable virological testing data, we cannot fit models accurately, or know confidently what the future of this epidemic will look like
  • and yet numbers are being presented to governments and the public with the appearance of certainty
  • Read Carefully and Trust Cautiously
  • Transparency: Look for how the data, technology, or recommendations are presented.
  • Thoughtfulness: Look for signs of hubris.
  • Example: Telenor
  • Expertise: Look for the professionals. Examine the credentials of those providing and processing the data.
  • Open Platforms: Look for the collaborators.
  • technology companies like Camber Systems, Cubeiq and Facebook have allowed scientists to examine their data,
  • The Covid-19 Mobility Data Network, of which we are part, comprises a voluntary collaboration of epidemiologists from around the world analyzes aggregated data from technology companies to provide daily insights to city and state officials from California to Dhaka, Bangladesh
  • This pandemic has been studied more intensely in a shorter amount of time than any other human event.
  •  
    "This pandemic has been studied more intensely in a shorter amount of time than any other human event. Our globalized world has rapidly generated and shared a vast amount of information about it. It is inevitable that there will be bad as well as good data in that mix. These massive, decentralized, and crowd-sourced data can reliably be converted to life-saving knowledge if tempered by expertise, transparency, rigor, and collaboration. When making your own decisions, read closely, trust carefully, and when in doubt, look to the experts."
Dennis OConnor

It's time for individuals to own their health data - STAT - 0 views

  •  
    Recommended by Tyler Orion - "For data from wearable technology to apps to text messaging, ownership is determined by the terms and conditions you agree to. The Apple Watch and Google Fitbit, for example, are both designed to give you access to key indicators of your health but their terms and conditions don't give you ownership of your data - and users don't know how their data are being used. This landscape is further complicated by the status of data under property law, which isn't viewed as wholly "ownable." And since current laws don't view people as the owners of their personal data, health care and service providers treat data as under their ownership. And those data are lucrative."
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)
  •  
    "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

Barbarians at the Gate: Consumer-Driven Health Data Commons and the Transformation of C... - 0 views

  •  
    "Current research and privacy regulations, which were designed for clinical research and for small-data studies of the past, cannot support creation of the vast data resources that 21st-century science needs. These regulations enshrine data-holders (hospitals, insurers, and other entities that store people's data) as the prime movers in assembling large-scale data resources for scientific use and rely on mechanisms - such as de-identification of data and waivers of individual consent - that are unworkable going forward. They shower individuals with unwanted, paternalistic protections - such as barriers to access to their own research results - while denying them a voice in what will be done with their data."
Dennis OConnor

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

  •  
    "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

Oura / TemPredict initial results: Feasibility of continuous fever monitoring using wea... - 0 views

  • we present early results from the first 50 subjects with enough data to meet analysis inclusion criteria
  •  
    "Abstract Elevated core temperature constitutes an important biomarker for COVID-19 infection; however, no standards currently exist to monitor fever using wearable peripheral temperature sensors. Evidence that sensors could be used to develop fever monitoring capabilities would enable large-scale health-monitoring research and provide high-temporal resolution data on fever responses across heterogeneous populations. We launched the TemPredict study in March of 2020 to capture continuous physiological data, including peripheral temperature, from a commercially available wearable device during the novel coronavirus pandemic. We coupled these data with symptom reports and COVID-19 diagnosis data. Here we report findings from the first 50 subjects who reported COVID-19 infections. These cases provide the first evidence that illness-associated elevations in peripheral temperature are observable using wearable devices and correlate with self-reported fever. Our analyses support the hypothesis that wearable sensors can detect illnesses in the absence of symptom recognition. Finally, these data support the hypothesis that prediction of illness onset is possible using continuously generated physiological data collected by wearable sensors. Our findings should encourage further research into the role of wearable sensors in public health efforts aimed at illness detection, and underscore the importance of integrating temperature sensors into commercially available wearables."
Dennis OConnor

Own Your Health Data - 1 views

  •  
    Recommended by Tyler Orion- "As the future of our healthcare system moves towards electronic healthcare records, we need patient data ownership rights to protect patient care. 4 Principles 1. Patients co-own or fully own every health data point about themselves. 2. Health data generated about the patient by a provider is co-owned by both parties. 3. Health data generated by the patient is fully owned by the patient with a right to possess, share, sell, or destroy. 4. All uses of a patients' health data shall be consented in advance by the patient, other than uses required by law."
Dennis OConnor

Data strategy for achieving a patient-centric future - Partner Content - 0 views

  •  
    "Life science companies seeking further advances toward a truly patient-centric future should consider working with an external partner that has extensive experience and a reliable, transparent and proven information portfolio. Leveraging core data linked and integrated with data generated by patients, and providing access to novel, on-demand data sources through a network of curated data partners provides enriched data that goes beyond the patient experience with a particular brand. By understanding the full details of the patient journey, optimal engagement of patients and HCPs can be enabled, thereby delivering the right treatment to the right patient, supporting adoption and adherence and achieving the ultimate goal of patient-centricity."
Dennis OConnor

Why we need a small data paradigm | BMC Medicine | Full Text - 0 views

  •  
    "There is great interest in and excitement about the concept of personalized or precision medicine and, in particular, advancing this vision via various 'big data' efforts. While these methods are necessary, they are insufficient to achieve the full personalized medicine promise. A rigorous, complementary 'small data' paradigm that can function both autonomously from and in collaboration with big data is also needed. By 'small data' we build on Estrin's formulation and refer to the rigorous use of data by and for a specific N-of-1 unit (i.e., a single person, clinic, hospital, healthcare system, community, city, etc.) to facilitate improved individual-level description, prediction and, ultimately, control for that specific unit."
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.
  • ...8 more annotations...
  • 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.
  •  
    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.
  •  
    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

Dr. Alex Cahana - Pain Expert Says Blockchain Tech Can Help Cure the Ills That Are Hurt... - 0 views

  • We don't need to create these huge data banks that can be hacked and manipulated
  • We don't need to bring the data to the algorithm, the algorithm can go to the data.
  • It is called federated learning which is like machine learning together with privacy-preserving technologies
  • ...4 more annotations...
  • introducing a whole token economy into healthcare
  • transform people from health service consumers to health and wealth producers
  • transforms digital healthcare from patient-centric to patient-driven
  • here is not only accountability between us, but an interdependence between us if we want all of us to survive and this is the world we are now moving into,
  •  
    "Cahana broke down the possibilities presented by distributed ledger technology. "Blockchain offers an operational environment that allows us to analyze data at its source. We don't need to create these huge data banks that can be hacked and manipulated. We don't need to bring the data to the algorithm, the algorithm can go to the data. It is called federated learning which is like machine learning together with privacy-preserving technologies," said Cahana. "The idea of introducing a whole token economy into healthcare is to transform people from health service consumers to health and wealth producers. As opposed to artificial intelligence (AI), machine learning, genomics, telemedicine, and all these things that are innovative and are general-purpose technologies that make things faster, better and cheaper, blockchain really is disruptive in the business model. It really transforms digital healthcare from patient-centric to patient-driven. People can drive their own health similar to how they invest in their wealth.""
Dennis OConnor

Wearable sensor data and self-reported symptoms for COVID-19 detection | Nature Medicine - 0 views

  •  
    "Abstract Traditional screening for COVID-19 typically includes survey questions about symptoms and travel history, as well as temperature measurements. Here, we explore whether personal sensor data collected over time may help identify subtle changes indicating an infection, such as in patients with COVID-19. We have developed a smartphone app that collects smartwatch and activity tracker data, as well as self-reported symptoms and diagnostic testing results, from individuals in the United States, and have assessed whether symptom and sensor data can differentiate COVID-19 positive versus negative cases in symptomatic individuals. We enrolled 30,529 participants between 25 March and 7 June 2020, of whom 3,811 reported symptoms. Of these symptomatic individuals, 54 reported testing positive and 279 negative for COVID-19. We found that a combination of symptom and sensor data resulted in an area under the curve (AUC) of 0.80 (interquartile range (IQR): 0.73-0.86) for discriminating between symptomatic individuals who were positive or negative for COVID-19, a performance that is significantly better (P 
Dennis OConnor

RARE-X A Patient Centric Approach to Consent.docx.pdf - 0 views

  •  
    RARE‐X is committed to transforming rare disease by ensuring that patient communities, clinicians, researchers, and drug developers have access to the right data at the right time. At the heart of RARE‐X's approach is a belief that patients should own their data. In July 2021, RARE‐X launched itsfirst set of rare disease pilot programs on its data collection platform supported by data governance and consent that will ensure participants who spend the time to enter their data are able to share it with those stakeholders they choose.
Dennis OConnor

Small Data, Where N = Me | April 2014 | Communications of the ACM - 0 views

  •  
    "We hear a lot about how big data, smart devices, and all the '-omics' (for example, genomics, proteomics, metabolomics, and so forth) are going to transform medicine-and they will. But there is another force that is going to change the way we think about and practice health, and that is our small data-small data derived from our individual digital traces."
Dennis OConnor

Gapminder - Hans Rosling's TED TALK Archive - 1 views

  •  
    Rosling and Gapminder creating stunning dynamic data visualizations of WHO (World Heath Organization) statistics. They are dedicated to proving with data the FACTS about our world. This is a way to a global view point that will help us all see that life on our planet is far better than it has ever been. Ready to use data to challenge your assumptions and shed your misconceptions? Dive in!
Dennis OConnor

GA4GH (Global Alliance for Genomics & Health) Community Response to COVID-19 - 0 views

  • A Message from the GA4GH Executive Committee Ewan Birney, Heidi Rehm, Peter Goodhand, and Kathryn North The urgency of scientific data sharing is never more apparent than during a global disease outbreak. Rapid sharing of high quality data is critical for the effective and timely response to any pandemic. GA4GH has joined Wellcome and others to call for rapid, open sharing of research findings and data relevant to COVID-19. The GA4GH community is responding through the development of a variety of research and data sharing platforms and initiatives…. But in order to ensure truly equitable access to and participation in both the scientific process and its benefits, we must rigorously maintain technical and ethical standards that support the open sharing of data and knowledge—now and always.
  •  
    Recommended by DeAunne Denmark, MD. Phd.
Dennis OConnor

LearnSphere - 0 views

  • LearnSphere integrates existing and new educational data and analysis repositories to offer the world's largest learning analytics infrastructure with methods, linked data, and portal access to relevant resources.
    • Dennis OConnor
       
      Query: Does UCSD use LearnSphere?
  •  
    "LearnSphere integrates existing and new educational data and analysis repositories to offer the world's largest learning analytics infrastructure with methods, linked data, and portal access to relevant resources." Stanford is working with the Tigris online workflow authoring tool. Need to explore this tool. No UCSD links?
Dennis OConnor

Picnic AI - 1 views

  •  
    "Every patient has a story Medicine used to be a one-size fits all model. Disease X meant treatment Y. Doctors made decisions and patients listened.  Clinical trials were our only data source. But those days are over. Medicine has gotten personal.   Today, we know  that every patient has a unique medical story. The best care requires knowing those stories and the next generation of medical discovery requires compiling those stories into structured data sets.   That's why PicnicHealth works directly with patients to gather and manage complete, up-to-date medical records. That's also why with our PicnicAI platform, we go beyond serving patients directly, and partner with the most innovative Life Sciences companies to sponsor PicnicHealth accounts for groups of research volunteers. Only by putting patients in control of their own data will we move beyond fragmented, unstructured medical records for both individual patient benefit today and for the opportunity to meaningfully contribute to tomorrow's medicine."
Dennis OConnor

This Is How We Beat the Coronavirus - The Atlantic - 1 views

  • We’re closing schools and businesses and committing to social (really, physical) distancing. But as the sobering charts from the analysis show, this isn’t enough.
  • Asian countries have engaged in suppression; we are only engaging in mitigation.
  • At the moment, we can’t even test everyone who is sick.
  • ...15 more annotations...
  • Testing will allow us to isolate the infected so they can’t infect others. We need to be vigilant, and willing to quarantine people with absolute diligence.
  • To achieve this, we need to test many, many people, even those without symptoms.
  • buried in the Imperial College report is reason for optimism. The analysis finds that in the do-nothing scenario, many people die and die quickly. With serious mitigation, though, many of the measures we’re taking now slow things down. By the summer, the report calculates, the number of people who become sick will eventually reduce to a trickle.
  • Our efforts are good, temporizing measures.
  • Social distancing cannot prevent these infections, as they’ve already happened. Therefore, things will appear to get worse for some time, even if what we’re doing is making things better in the long run.
  • Our primary approach is social distancing—asking people to stay away from one another.
  • We can create a third path. We can decide to meet this challenge head-on. It is absolutely within our capacity to do so. We could develop tests that are fast, reliable, and ubiquitous. If we screen everyone, and do so regularly, we can let most people return to a more normal life. We can reopen schools and places where people gather. If we can be assured that the people who congregate aren’t infectious, they can socialize.
  • We can build health-care facilities that do rapid screening and care for people who are infected, apart from those who are not.
  • We can even commit to housing infected people apart from their healthy family members, to prevent transmission in households.
  • We will need to massively strengthen our medical infrastructure. We will need to build ventilators and add hospital beds. We will need to train and redistribute physicians, nurses, and respiratory therapists to where they are most needed. We will need to focus our factories on turning out the protective equipment—masks, gloves, gowns, and so forth—to ensure we keep our health-care workforce safe.
  • most importantly, we need to pour vast sums of intellectual and financial resources into developing a vaccine that would finally bring this nightmare to a close
  • If we commit to social distancing, however, at some point in the next few months the rate of spread will slow. We’ll be able to catch our breath. We’ll be able to ease restrictions, as some early hit countries are doing. We can move toward some semblance of normalcy.
  • The temptation then will be to think we have made it past the worst. We cannot give in to that temptation. That will be the time to redouble our efforts. We will need to prepare for the coming storm. We’ll need to build up our stockpiles, create strategies, and get ready.
  • We need to keep time on the clock, time to find a treatment or a vaccine.
  • We all have a choice to make. We can look at the coming fire and let it burn. We can hunker down, and hope to wait it out—or we can work together to get through it with as little damage as possible.
1 - 20 of 195 Next › Last »
Showing 20 items per page