4,370 Matching Annotations
  1. Last 7 days
    1. 2020-04-30

    2. Net-COVID Session4A: Math Models of Epidemic Spreading in the Time of COVID-19 by Ginestra Bianconi. (2020, May 1). https://www.youtube.com/watch?v=vZ2Ezsffkqs&list=PLVWaQYnj_BZVQal-KQ0rf8CcZJPIhpuO3&index=4

    3. Fourth lecture (seminar) of the Net-COVID online series: Understanding and Exploring Network Epidemiology in the Time of Coronavirus. Seminar by Ginestra Bianconi of Queen Mary University of London. See go.umd.edu/net-covid for more information about the online series.
    4. Net-COVID Session4A: Math Models of Epidemic Spreading in the Time of COVID-19 by Ginestra Bianconi
    1. DataBeers Torino // Covid-19 online edition. (2020, April 23). https://www.youtube.com/watch?v=g4QPqPFUZLc

    2. 2020-04-23

    3. Nel corso del primo DataBeers Torino interamente online, Michele Tizzoni -co-founder dell'iniziativa e Research Leader presso Fondazione ISI - presenta i risultati dello studio in cui è stato misurato l'impatto sulla la mobilità degli Italiani in seguito all'epidemia di COVID-19 e alle restrizioni imposte dal governo.
    4. DataBeers Torino // Covid-19 online edition
    1. Calm amid COVID. (2020, April). Berkeley News. Retrieved July 10, 2020, from https://news.berkeley.edu/topics/calm-amid-covid/

    2. 2020-04

    3. In touching every aspect of our lives, the COVID-19 pandemic has profoundly disrupted our sense of well-being and produced uncertainty and anxiety. How do we find resilience while remaining productive and caring family members, friends, professionals and citizens in these unprecedented times? In a series of ten short videos (one video will be added per week until mid-June, 2020), UC Berkeley psychologist Dacher Keltner, who has studied stress, relationships and well-being for 25 years and is co-founder of the campus’s Greater Good Science Center, will share ideas and practices for cultivating resilience and connection as we face the challenges of the coming months. Drawing on insights from the center’s Science of Happiness online course, podcast series and magazine, Keltner shares tips on how to manage stress and find meaningful connections while social distancing, completing each video with simple, science-tested practices useful for this moment in time.
    4. Calm amid COVID
  2. Jul 2020
    1. 2020-05-26

    2. Dr Daniel Quintana | Using Twitter for Science | R.I.O.T. Science Club—YouTube. (2020, May 26). https://www.youtube.com/watch?v=pA5Y4cO934I

    3. Daniel Quintana will cover why social media skills are crucial for researchers and provide practical tips for how Twitter can be used to keep up-to-date with emerging methods, find new collaborators, and share your work with a global community of scientists. Daniel also touches on how Twitter can help scientists overcome gatekeeping in academia, and promote reproducible and open research.
    4. Dr Daniel Quintana | Using Twitter for Science | R.I.O.T. Science Club
    1. British Psychological Society rt Local Government Association (2020, May 20). "#MentalHealthAwarenessWeek: our webinar will explore the mental health impacts of #COVID19 across the life course & share how councils are working with partners to support public mental health and wellbeing. Join us on Thursday → http://socsi.in/gtRTr #CouncilsCan." Twitter. https://twitter.com/bpsofficial/status/1263113183373463553

    2. #MentalHealthAwarenessWeek: our webinar will explore the mental health impacts of #COVID19 across the life course & share how councils are working with partners to support public mental health and wellbeing. Join us on Thursday → http://socsi.in/gtRTr
  3. Jun 2020
    1. EU Datathon 2020—Webinar on COVID-19 and media and data monitoring. (2020, April 22). https://www.youtube.com/watch?v=wyNgmEfi_vk&feature=youtu.be

    2. 2020-04-22

    3. The goal of this webinar is to present specific data on COVID-19 to help tackle the global pandemic we are facing. We encourage participants to use these new datasets to develop apps in that domain, suitable for all the challenges of the competition (Challenge 1, 2, 3 and 4)
    4. EU Datathon 2020 - Webinar on COVID-19 and media and data monitoring
    1. Maintaining health and wellbeing during the COVID-19 pandemic | Institute of Psychiatry, Psychology & Neuroscience | King’s College London. https://www.kcl.ac.uk/ioppn/maintaining-health-and-wellbeing-during-the-covid-19-pandemic

    2. During a pandemic outbreak, how can we try and keep ourselves mentally and physically well? This is the question the Division of Psychology at the IoPPN answered in a series of talks at our virtual event 'Maintaining health and wellbeing during the COVID-19 pandemic' on 2 April 2020. Below, you will find video recordings of all of the talks.
    3. Maintaining health and wellbeing during the COVID-19 pandemic
    1. 2020-06-24

    2. Minocher, R., Atmaca, S., Bavero, C., McElreath, R., & Beheim, B. (2020, June 24). Reproducibility of social learning research declines exponentially over 63 years of publication. https://doi.org/10.31234/osf.io/4nzc7

    3. 10.31234/osf.io/4nzc7
    4. Interest in improving reproducibility, replicability and transparency of research has increased substantially across scientific fields over the last few decades. We surveyed 560 empirical, quantitative publications published between 1955 and 2018, to estimate the rate of reproducibility for research on social learning, a large subfield of behavioural ecology. We found supporting materials were available for less than 30% of publications during this period. The availability of data declines exponentially with time since publication, with a half-life of about six years, and this “data decay rate” varies systematically with both study design and study species. Conditional on materials being available, we estimate that a reasonable researcher could expect to successfully reproduce about 80% of published results, based on our evaluating a subset of 40 publications. Taken together, this indicates an overall success rate of 24% for both acquiring materials and recovering published results, with non- reproducibility of results primarily due to unavailable, incomplete, or poorly documented data. We provide recommendations to improve the reproducibility of research on the ecology and evolution of social behaviour.
    5. Reproducibility of social learning research declines exponentially over 63 years of publication
    1. 2020-06-24

    2. Saltelli, A., Bammer, G., Bruno, I., Charters, E., Di Fiore, M., Didier, E., Nelson Espeland, W., Kay, J., Lo Piano, S., Mayo, D., Pielke Jr, R., Portaluri, T., Porter, T. M., Puy, A., Rafols, I., Ravetz, J. R., Reinert, E., Sarewitz, D., Stark, P. B., … Vineis, P. (2020). Five ways to ensure that models serve society: A manifesto. Nature, 582(7813), 482–484. https://doi.org/10.1038/d41586-020-01812-9

    3. 10.1038/d41586-020-01812-9
    4. Pandemic politics highlight how predictions need to be transparent and humble to invite insight, not blame.
    5. Five ways to ensure that models serve society: a manifesto
    1. 2020-06-23

    2. Palayew, A., Norgaard, O., Safreed-Harmon, K. et al. Pandemic publishing poses a new COVID-19 challenge. Nat Hum Behav (2020). https://doi.org/10.1038/s41562-020-0911-0

    3. 10.1038/s41562-020-0911-0
    4. The scientific community’s response to COVID-19 has resulted in a large volume of research moving through the publication pipeline at extraordinary speed, with a median time from receipt to acceptance of 6 days for journal articles. Although the nature of this emergency warrants accelerated publishing, measures are required to safeguard the integrity of scientific evidence.
    5. Pandemic publishing poses a new COVID-19 challenge
    1. 2020-06-24

    2. Page Le, M. (2020, June 24). Town in UK takes steps to test entire population for coronavirus. New Scientist. https://www.newscientist.com/article/2246880-town-in-uk-takes-steps-to-test-entire-population-for-coronavirus/

    3. A town in the UK is about to start testing thousands of people for the coronavirus each week, using easily collected saliva and a cheap, quick way of detecting the virus. If the initial trial in Southampton is successful, the aim is to test the town’s entire population of 250,000 people every week to see if this can rapidly halt the virus’ spread.
    4. Town in UK takes steps to test entire population for coronavirus
    1. 2020-06-19

    2. Sharma, N., Uttrani, S., & Dutt, V. (2020, June 19). Modeling the Absence of Framing Effect in an Experience-based Covid-19 Disease Problem. 18th Annual Meeting of the International Conference on Cognitive Modelling. https://www.researchgate.net/publication/342313460_Modeling_the_Absence_of_Framing_Effect_in_an_Experience-based_Covid-19_Disease_Problem

    3. Prior research in decisions from experience (DFE) has investigated people's consequential decisions after information search both experimentally and computationally. However, prior DFE research has yet to explore how computational cognitive models and their mechanisms could explain the effects of problem framing in experience. The primary objective of this paper is to address this literature gap and develop Instance-based Learning Theory (IBLT) models on the effects of problem framing. Human data was collected on a modified form of the Asian disease problem posed about the COVID-19 pandemic across two between-subject conditions: gain (N = 40) and loss (N = 40). The COVID-19 problem was presented as "lives saved" in the gain condition and "lives lost" in the loss condition. Results revealed the absence of the classical framing effect, exhibiting no preference reversal between gain and loss conditions in experience. Next, an IBL model was developed and calibrated to the data obtained in the gain and loss problems. The calibrated model was generalized to the non-calibrated conditions (gain to loss and loss to gain). An IBL model with ACT-R default parameters was also generalized. Results revealed that the IBL model with calibrated parameters explained human choices more accurately compared to the IBL model with ACT-R default parameters. Also, participants showed greater reliance on recency and frequency of outcomes and less variability in their choices across both gain and loss conditions. We highlight the main implications of our findings for the cognitive modeling community.
    4. Modeling the Absence of Framing Effect in an Experience-based Covid-19 Disease Problem
    1. 2020-06-21

    2. Independent SAGE. (2020, June 21). "NEW: Independent SAGE has evaluated the scientific evidence on social distancing & concludes it is not safe to reduce it from 2m to 1m indoors as government proposes". Twitter. https://twitter.com/IndependentSage/status/1274729064272670721

    3. BAME & low-paid groups at particular risk as disproportionate number unable to work at home & exposed to greater risk under new rules expected to be announced Tues. Independent SAGE says govt must release underlying evidence so public & businesses can make own risk assessments
    4. Independent SAGE agrees with government’s own SAGE group that current levels of transmission are too high. Reducing rules from 2m to 1m will effectively end all social distancing in UK. It is too soon to do so.
    5. NEW: Independent SAGE has evaluated the scientific evidence on social distancing & concludes it is not safe to reduce it from 2m to 1m indoors as government proposes
    1. 2020-04-30

    2. Yeolekar, M. (2020, April 30). The Digital Migration: Lessons About Open Science Arising from the COVID19 Crisis. The Official PLOS Blog. https://theplosblog.plos.org/2020/04/the-digital-migration-lessons-about-open-science-arising-from-the-covid19-crisis/

    3. In the wake of COVID19, the world is scrambling to figure out how to continue the functions of normal life while confined to a much smaller world of couches and home offices. Work, family and friend relationships, exercise, entertainment, and all the other elements of normalcy have been upended. The effort to maintain productivity (and, to be frank, sanity) has initiated a mass digital migration; a movement from life to e-life.
    4. The Digital Migration: Lessons About Open Science Arising from the COVID19 Crisis
    1. 2010-01-17

    2. Hiatt, J., Patwardhan, R., Turner, E. et al. Parallel, tag-directed assembly of locally derived short sequence reads. Nat Methods 7, 119–122 (2010). https://doi.org/10.1038/nmeth.1416

    3. 10.1038/nmeth.1416
    4. We demonstrate subassembly, an in vitro library construction method that extends the utility of short-read sequencing platforms to applications requiring long, accurate reads. A long DNA fragment library is converted to a population of nested sublibraries, and a tag sequence directs grouping of short reads derived from the same long fragment, enabling localized assembly of long fragment sequences. Subassembly may facilitate accurate de novo genome assembly and metagenome sequencing.
    5. Parallel, tag-directed assembly of locally derived short sequence reads
    1. NA

    2. Interactive Heat Map - SARS-CoV-2 - Bloom Lab

    3. Instructions Hover over cells with mouse to reveal additional information. Select site subsets using the drop down menu below the plots. Change which sites are displayed by brushing the zoom bar and dragging the brush. Clear the zoom bar by double clicking it. Structural visualizations of the data are available via dms-view here See the paper describing these data here Raw data available on GitHub
    4. SARS-CoV-2 RBD DMS
    1. 2020-06-17

    2. Starr, T. N., Greaney, A. J., Hilton, S. K., Crawford, K. H., Navarro, M. J., Bowen, J. E., Tortorici, M. A., Walls, A. C., Veesler, D., & Bloom, J. D. (2020). Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding [Preprint]. Microbiology. https://doi.org/10.1101/2020.06.17.157982

    3. 10.1101/2020.06.17.157982
    4. The receptor binding domain (RBD) of the SARS-CoV-2 spike glycoprotein mediates viral attachment to ACE2 receptor, and is a major determinant of host range and a dominant target of neutralizing antibodies. Here we experimentally measure how all amino-acid mutations to the RBD affect expression of folded protein and its affinity for ACE2. Most mutations are deleterious for RBD expression and ACE2 binding, and we identify constrained regions on the RBD's surface that may be desirable targets for vaccines and antibody-based therapeutics. But a substantial number of mutations are well tolerated or even enhance ACE2 binding, including at ACE2 interface residues that vary across SARS-related coronaviruses. However, we find no evidence that these ACE2-affinity enhancing mutations have been selected in current SARS-CoV-2 pandemic isolates. We present an interactive visualization and open analysis pipeline to facilitate use of our dataset for vaccine design and functional annotation of mutations observed during viral surveillance.
    5. Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding
    1. 2020-06-18

    2. Bloom Lab. (2020, June 18). "We've experimentally measured how all amino-acid mutations to the #SARSCoV2 spike RBD affect ACE2 binding and expression of folded protein in a deep mutational scanning study led by @tylernstarr & Allie Greaney:https://biorxiv.org/content/10.1101/2020.06.17.157982v1 Why is this important? (1/n)" Twitter. https://twitter.com/jbloom_lab/status/1273468539484213248

    3. Now we hope data we generated will help others studying evolution of virus and especially those developing vaccines. It's all publicly available, so if you're curious about a specific mutation to RBD, need a stabilizing mutation, or need to change a surface--go look it up! (14/n)
    4. Allie Greaney jumped on board to help @tylernstarr do the experiments amazingly fast, and Sarah Hilton and @khdcrawford helped with code and validation. (13/n)
    5. @tylernstarr had been optimizing approach for other proteins when #SARS_CoV2 hit. We had as colleagues @veeslerlab @coronalexington who had been building basic knowledge about coronavirus spikes for years. They helped advise @tylernstarr how to adapt his approach to RBD. (12/n)
    6. To enable these deep mutational scanning titration assays to be applied to larger protein like RBD, we leveraged barcoding approach originally developed by @JShendure and subsequently extended to use PacBio by @lea_starita @kmatreyek @dougfowler42: https://nature.com/articles/nmeth.1416… (11/n)
    7. Finally, how we were able to characterize so many mutations to this important protein? We leveraged great prior work. In 2016, @jbkinney, Walczak, & Mora showed yeast display & deep mutational scanning could measure dissociation constants at scale: https://elifesciences.org/articles/23156 (10/n)
    8. Lots of other observations about natural mutations, structure-function, and sarbecovirus evolution in the paper itself, so take a look. (9/n)
    9. Key finding from that comparison is that no antibodies have epitopes as constrained as actual ACE2. So epitope focusing can elicit more escape-resistant antibodies. And our data help point the way, as we show what mutations would be tolerated in resurfaced immunogens! (8/n)
    10. We can examine mutational tolerance of epitopes of different antibodies, and compare it to mutational tolerance of actual ACE2 binding interface (here are some antibodies, see paper for more). (7/n)
    11. We can map tolerance to mutations with respect to RBD folding / expression & ACE2 binding on structure (red = intolerant in images below). As expected, most selection for binding in ACE2 interface--but again, lots of mutations still tolerated (again see heat maps or paper) (6/n)
    12. Some observations: While many mutations to RBD are deleterious, lots are tolerated--including a surprising number that increase ACE2 affinity (blue in heat map in prior Tweet). But no evidence that strong affinity enhancing mutations are being selected in human isolates. (5/n)
    13. If you're interested in the evolution of the virus or are studying antibodies / vaccines, you can go to this interactive heatmap (https://jbloomlab.github.io/SARS-CoV-2-RBD_DMS/…) and simply look up the *experimentally measured* effect of any mutation. (4/n)
    14. Before our study, the structure of the RBD protein was known but we didn't know how mutations affected it's function. Now we've measured how virtually all (3800 of 3819) amino-acid mutations affect binding to ACE2 and expression of the folded protein. (3/n)
    15. The RBD (receptor binding domain) enables #SARSCoV2 to bind to human cells. Evolution to bind human ACE2 was key to the emergence of this virus. Now it's also key to mitigating the virus: the most potent antibodies bind to RBD, and most vaccine candidates contain RBD. (2/n)
    16. We've experimentally measured how all amino-acid mutations to the #SARSCoV2 spike RBD affect ACE2 binding and expression of folded protein in a deep mutational scanning study led by @tylernstarr & Allie Greaney: https://biorxiv.org/content/10.1101/2020.06.17.157982v1… Why is this important? (1/n)
    1. NA

    2. Vincent-Lamarre, P., Sugimoto, C.R., & Larivière, V. (n.d.). Monitoring women's scholarly production during the COVID-19 pandemic. Shiny.initiativesnumeriques.org. http://shiny.initiativesnumeriques.org/monitoring-scholarly-covid/

    3. Given the significant uptake in the incentives and use of preprints and registered reports, a few early analyses have used those to document the phenomenon: women economists were shown to have a drop in production of preprints and registered reports in March and April and were less likely to work on COVID-related topics. Similarly, over the last three months male authors on arXiv and bioRxiv increased at a greater rate than women authors. Our own analysis builds on data from 11 pre-print repositories and three platforms, for a total of 327,902 documents. This work demonstrates the disproportionate effect on early career researchers (using authorship position as a proxy for seniority in science). We have created this dynamic and interactive website to allow policy makers, scientists, and administrators to monitor this evolving situation. As of May 18th 2020, the data covers 284,842 pre-prints and registered reports, which will be updated on a regular basis.
    4. Monitoring women's scholarly production during the COVID-19 pandemic
    1. 2020-06-19

    2. McCartney, M. (2020, June 19). "profound disconnect between the government belief about what benefits technology will provide, and the later (after ££) evidence for benefit. tech in health=vital, but if not fit for purpose ends up wasting resources better spent elsewhere- time+money. what needs to change?" Twitter. https://twitter.com/mgtmccartney/status/1273878159184756736

    3. and last. government needs to use expertise on the ground. patient voices and organisations are really important here. yet seem scarcely used as a resource to help get this right. trust is not bought, is built. off to work
    4. the second is false advertising. this should always been a red flag and needs to stop. no one in the NHS should trust any org/ provider who makes surreal claims about their stuff or who gets shirty when ask for evidence. yes, am talking about you @babylonhealth
    5. the best tech has grown stuff from ground up and found out what is needed and wanted and what works. humility to know there's stuff you don't yet know. understanding that NHS staff can't be left fixing your botched rubbish.