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name="searchtype"><option value="all">All fields</option><option value="title">Title</option><option selected value="author">Author(s)</option><option value="abstract">Abstract</option><option value="comments">Comments</option><option value="journal_ref">Journal reference</option><option value="acm_class">ACM classification</option><option value="msc_class">MSC classification</option><option value="report_num">Report number</option><option value="paper_id">arXiv identifier</option><option value="doi">DOI</option><option value="orcid">ORCID</option><option value="license">License (URI)</option><option value="author_id">arXiv author ID</option><option value="help">Help pages</option><option value="full_text">Full text</option></select> <input id="query" name="query" type="text" value="Riley, S"> <ul id="abstracts"><li><input checked id="abstracts-0" name="abstracts" type="radio" value="show"> <label for="abstracts-0">Show abstracts</label></li><li><input id="abstracts-1" name="abstracts" type="radio" value="hide"> <label for="abstracts-1">Hide abstracts</label></li></ul> </div> <div class="box field is-grouped is-grouped-multiline level-item"> <div class="control"> <span class="select is-small"> <select id="size" name="size"><option value="25">25</option><option selected value="50">50</option><option value="100">100</option><option value="200">200</option></select> </span> <label for="size">results per page</label>. </div> <div class="control"> <label for="order">Sort results by</label> <span class="select is-small"> <select id="order" name="order"><option selected value="-announced_date_first">Announcement date (newest first)</option><option value="announced_date_first">Announcement date (oldest first)</option><option value="-submitted_date">Submission date (newest first)</option><option value="submitted_date">Submission date (oldest first)</option><option value="">Relevance</option></select> </span> </div> <div class="control"> <button class="button is-small is-link">Go</button> </div> </div> </form> </div> </div> <ol class="breathe-horizontal" start="1"> <li class="arxiv-result"> <div class="is-marginless"> <p class="list-title is-inline-block"><a href="https://arxiv.org/abs/2311.13724">arXiv:2311.13724</a> <span> [<a href="https://arxiv.org/pdf/2311.13724">pdf</a>] </span> </p> <div class="tags is-inline-block"> <span class="tag is-small is-link tooltip is-tooltip-top" data-tooltip="Computers and Society">cs.CY</span> <span class="tag is-small is-grey tooltip is-tooltip-top" data-tooltip="Physics and Society">physics.soc-ph</span> <span class="tag is-small is-grey tooltip is-tooltip-top" data-tooltip="Populations and Evolution">q-bio.PE</span> </div> </div> <p class="title is-5 mathjax"> Infectious disease surveillance needs for the United States: lessons from COVID-19 </p> <p class="authors"> <span class="search-hit">Authors:</span> <a href="/search/q-bio?searchtype=author&query=Lipsitch%2C+M">Marc Lipsitch</a>, <a href="/search/q-bio?searchtype=author&query=Bassett%2C+M+T">Mary T. Bassett</a>, <a href="/search/q-bio?searchtype=author&query=Brownstein%2C+J+S">John S. Brownstein</a>, <a href="/search/q-bio?searchtype=author&query=Elliott%2C+P">Paul Elliott</a>, <a href="/search/q-bio?searchtype=author&query=Eyre%2C+D">David Eyre</a>, <a href="/search/q-bio?searchtype=author&query=Grabowski%2C+M+K">M. Kate Grabowski</a>, <a href="/search/q-bio?searchtype=author&query=Hay%2C+J+A">James A. Hay</a>, <a href="/search/q-bio?searchtype=author&query=Johansson%2C+M">Michael Johansson</a>, <a href="/search/q-bio?searchtype=author&query=Kissler%2C+S+M">Stephen M. Kissler</a>, <a href="/search/q-bio?searchtype=author&query=Larremore%2C+D+B">Daniel B. Larremore</a>, <a href="/search/q-bio?searchtype=author&query=Layden%2C+J">Jennifer Layden</a>, <a href="/search/q-bio?searchtype=author&query=Lessler%2C+J">Justin Lessler</a>, <a href="/search/q-bio?searchtype=author&query=Lynfield%2C+R">Ruth Lynfield</a>, <a href="/search/q-bio?searchtype=author&query=MacCannell%2C+D">Duncan MacCannell</a>, <a href="/search/q-bio?searchtype=author&query=Madoff%2C+L+C">Lawrence C. Madoff</a>, <a href="/search/q-bio?searchtype=author&query=Metcalf%2C+C+J+E">C. Jessica E. Metcalf</a>, <a href="/search/q-bio?searchtype=author&query=Meyers%2C+L+A">Lauren A. Meyers</a>, <a href="/search/q-bio?searchtype=author&query=Ofori%2C+S+K">Sylvia K. Ofori</a>, <a href="/search/q-bio?searchtype=author&query=Quinn%2C+C">Celia Quinn</a>, <a href="/search/q-bio?searchtype=author&query=Bento%2C+A+I+R">Ana I. Ramos Bento</a>, <a href="/search/q-bio?searchtype=author&query=Reich%2C+N">Nick Reich</a>, <a href="/search/q-bio?searchtype=author&query=Riley%2C+S">Steven Riley</a>, <a href="/search/q-bio?searchtype=author&query=Rosenfeld%2C+R">Roni Rosenfeld</a>, <a href="/search/q-bio?searchtype=author&query=Samore%2C+M+H">Matthew H. Samore</a>, <a href="/search/q-bio?searchtype=author&query=Sampath%2C+R">Rangarajan Sampath</a> , et al. (5 additional authors not shown) </p> <p class="abstract mathjax"> <span class="has-text-black-bis has-text-weight-semibold">Abstract</span>: <span class="abstract-short has-text-grey-dark mathjax" id="2311.13724v1-abstract-short" style="display: inline;"> The COVID-19 pandemic has highlighted the need to upgrade systems for infectious disease surveillance and forecasting and modeling of the spread of infection, both of which inform evidence-based public health guidance and policies. Here, we discuss requirements for an effective surveillance system to support decision making during a pandemic, drawing on the lessons of COVID-19 in the U.S., while l… <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2311.13724v1-abstract-full').style.display = 'inline'; document.getElementById('2311.13724v1-abstract-short').style.display = 'none';">▽ More</a> </span> <span class="abstract-full has-text-grey-dark mathjax" id="2311.13724v1-abstract-full" style="display: none;"> The COVID-19 pandemic has highlighted the need to upgrade systems for infectious disease surveillance and forecasting and modeling of the spread of infection, both of which inform evidence-based public health guidance and policies. Here, we discuss requirements for an effective surveillance system to support decision making during a pandemic, drawing on the lessons of COVID-19 in the U.S., while looking to jurisdictions in the U.S. and beyond to learn lessons about the value of specific data types. In this report, we define the range of decisions for which surveillance data are required, the data elements needed to inform these decisions and to calibrate inputs and outputs of transmission-dynamic models, and the types of data needed to inform decisions by state, territorial, local, and tribal health authorities. We define actions needed to ensure that such data will be available and consider the contribution of such efforts to improving health equity. <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2311.13724v1-abstract-full').style.display = 'none'; document.getElementById('2311.13724v1-abstract-short').style.display = 'inline';">△ Less</a> </span> </p> <p class="is-size-7"><span class="has-text-black-bis has-text-weight-semibold">Submitted</span> 22 November, 2023; <span class="has-text-black-bis has-text-weight-semibold">originally announced</span> November 2023. </p> </li> <li class="arxiv-result"> <div class="is-marginless"> <p class="list-title is-inline-block"><a href="https://arxiv.org/abs/2307.03415">arXiv:2307.03415</a> <span> [<a href="https://arxiv.org/pdf/2307.03415">pdf</a>, <a href="https://arxiv.org/format/2307.03415">other</a>] </span> </p> <div class="tags is-inline-block"> <span class="tag is-small is-link tooltip is-tooltip-top" data-tooltip="Populations and Evolution">q-bio.PE</span> <span class="tag is-small is-grey tooltip is-tooltip-top" data-tooltip="Quantitative Methods">q-bio.QM</span> </div> </div> <p class="title is-5 mathjax"> Differences between the true reproduction number and the apparent reproduction number of an epidemic time series </p> <p class="authors"> <span class="search-hit">Authors:</span> <a href="/search/q-bio?searchtype=author&query=Eales%2C+O">Oliver Eales</a>, <a href="/search/q-bio?searchtype=author&query=Riley%2C+S">Steven Riley</a> </p> <p class="abstract mathjax"> <span class="has-text-black-bis has-text-weight-semibold">Abstract</span>: <span class="abstract-short has-text-grey-dark mathjax" id="2307.03415v1-abstract-short" style="display: inline;"> The time-varying reproduction number $R(t)$ measures the number of new infections per infectious individual and is closely correlated with the time series of infection incidence by definition. The timings of actual infections are rarely known, and analysis of epidemics usually relies on time series data for other outcomes such as symptom onset. A common implicit assumption, when estimating $R(t)$… <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2307.03415v1-abstract-full').style.display = 'inline'; document.getElementById('2307.03415v1-abstract-short').style.display = 'none';">▽ More</a> </span> <span class="abstract-full has-text-grey-dark mathjax" id="2307.03415v1-abstract-full" style="display: none;"> The time-varying reproduction number $R(t)$ measures the number of new infections per infectious individual and is closely correlated with the time series of infection incidence by definition. The timings of actual infections are rarely known, and analysis of epidemics usually relies on time series data for other outcomes such as symptom onset. A common implicit assumption, when estimating $R(t)$ from an epidemic time series, is that $R(t)$ has the same relationship with these downstream outcomes as it does with the time series of incidence. However, this assumption is unlikely to be valid given that most epidemic time series are not perfect proxies of incidence. Rather they represent convolutions of incidence with uncertain delay distributions. Here we define the apparent time-varying reproduction number, $R_A(t)$, the reproduction number calculated from a downstream epidemic time series and demonstrate how differences between $R_A(t)$ and $R(t)$ depend on the convolution function. The mean of the convolution function sets a time offset between the two signals, whilst the variance of the convolution function introduces a relative distortion between them. We present the convolution functions of epidemic time series that were available during the SARS-CoV-2 pandemic. Infection prevalence, measured by random sampling studies, presents fewer biases than other epidemic time series. Here we show that additionally the mean and variance of its convolution function were similar to that obtained from traditional surveillance based on mass-testing and could be reduced using more frequent testing, or by using stricter thresholds for positivity. Infection prevalence studies continue to be a versatile tool for tracking the temporal trends of $R(t)$, and with additional refinements to their study protocol, will be of even greater utility during any future epidemics or pandemics. <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2307.03415v1-abstract-full').style.display = 'none'; document.getElementById('2307.03415v1-abstract-short').style.display = 'inline';">△ Less</a> </span> </p> <p class="is-size-7"><span class="has-text-black-bis has-text-weight-semibold">Submitted</span> 7 July, 2023; <span class="has-text-black-bis has-text-weight-semibold">originally announced</span> July 2023. </p> </li> <li class="arxiv-result"> <div class="is-marginless"> <p class="list-title is-inline-block"><a href="https://arxiv.org/abs/2306.01224">arXiv:2306.01224</a> <span> [<a href="https://arxiv.org/pdf/2306.01224">pdf</a>] </span> </p> <div class="tags is-inline-block"> <span class="tag is-small is-link tooltip is-tooltip-top" data-tooltip="Physics and Society">physics.soc-ph</span> <span class="tag is-small is-grey tooltip is-tooltip-top" data-tooltip="Quantitative Methods">q-bio.QM</span> </div> </div> <p class="title is-5 mathjax"> Key challenges for the surveillance of respiratory viruses: transitioning out of the acute phase of the SARS-CoV-2 pandemic </p> <p class="authors"> <span class="search-hit">Authors:</span> <a href="/search/q-bio?searchtype=author&query=Eales%2C+O">Oliver Eales</a>, <a href="/search/q-bio?searchtype=author&query=Plank%2C+M+J">Michael J. Plank</a>, <a href="/search/q-bio?searchtype=author&query=Cowling%2C+B+J">Benjamin J. Cowling</a>, <a href="/search/q-bio?searchtype=author&query=Howden%2C+B+P">Benjamin P. Howden</a>, <a href="/search/q-bio?searchtype=author&query=Kucharski%2C+A+J">Adam J. Kucharski</a>, <a href="/search/q-bio?searchtype=author&query=Sullivan%2C+S+G">Sheena G. Sullivan</a>, <a href="/search/q-bio?searchtype=author&query=Vandemaele%2C+K">Katelijn Vandemaele</a>, <a href="/search/q-bio?searchtype=author&query=Viboud%2C+C">Cecile Viboud</a>, <a href="/search/q-bio?searchtype=author&query=Riley%2C+S">Steven Riley</a>, <a href="/search/q-bio?searchtype=author&query=McCaw%2C+J+M">James M. McCaw</a>, <a href="/search/q-bio?searchtype=author&query=Shearer%2C+F+M">Freya M. Shearer</a> </p> <p class="abstract mathjax"> <span class="has-text-black-bis has-text-weight-semibold">Abstract</span>: <span class="abstract-short has-text-grey-dark mathjax" id="2306.01224v1-abstract-short" style="display: inline;"> To support the ongoing management of viral respiratory diseases, many countries are moving towards an integrated model of surveillance for SARS-CoV-2, influenza, and other respiratory pathogens. While many surveillance approaches catalysed by the COVID-19 pandemic provide novel epidemiological insight, continuing them as implemented during the pandemic is unlikely to be feasible for non-emergency… <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2306.01224v1-abstract-full').style.display = 'inline'; document.getElementById('2306.01224v1-abstract-short').style.display = 'none';">▽ More</a> </span> <span class="abstract-full has-text-grey-dark mathjax" id="2306.01224v1-abstract-full" style="display: none;"> To support the ongoing management of viral respiratory diseases, many countries are moving towards an integrated model of surveillance for SARS-CoV-2, influenza, and other respiratory pathogens. While many surveillance approaches catalysed by the COVID-19 pandemic provide novel epidemiological insight, continuing them as implemented during the pandemic is unlikely to be feasible for non-emergency surveillance, and many have already been scaled back. Furthermore, given anticipated co-circulation of SARS-CoV-2 and influenza, surveillance activities in place prior to the pandemic require review and adjustment to ensure their ongoing value for public health. In this perspective, we highlight key challenges for the development of integrated models of surveillance. We discuss the relative strengths and limitations of different surveillance practices and studies, their contribution to epidemiological assessment, forecasting, and public health decision making. <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2306.01224v1-abstract-full').style.display = 'none'; document.getElementById('2306.01224v1-abstract-short').style.display = 'inline';">△ Less</a> </span> </p> <p class="is-size-7"><span class="has-text-black-bis has-text-weight-semibold">Submitted</span> 1 June, 2023; <span class="has-text-black-bis has-text-weight-semibold">originally announced</span> June 2023. </p> </li> <li class="arxiv-result"> <div class="is-marginless"> <p class="list-title is-inline-block"><a href="https://arxiv.org/abs/2102.05445">arXiv:2102.05445</a> <span> [<a href="https://arxiv.org/pdf/2102.05445">pdf</a>] </span> </p> <div class="tags is-inline-block"> <span class="tag is-small is-link tooltip is-tooltip-top" data-tooltip="Computers and Society">cs.CY</span> <span class="tag is-small is-grey tooltip is-tooltip-top" data-tooltip="Social and Information Networks">cs.SI</span> <span class="tag is-small is-grey tooltip is-tooltip-top" data-tooltip="Physics and Society">physics.soc-ph</span> <span class="tag is-small is-grey tooltip is-tooltip-top" data-tooltip="Populations and Evolution">q-bio.PE</span> </div> </div> <p class="title is-5 mathjax"> Epidemiological and public health requirements for COVID-19 contact tracing apps and their evaluation </p> <p class="authors"> <span class="search-hit">Authors:</span> <a href="/search/q-bio?searchtype=author&query=Colizza%2C+V">Vittoria Colizza</a>, <a href="/search/q-bio?searchtype=author&query=Grill%2C+E">Eva Grill</a>, <a href="/search/q-bio?searchtype=author&query=Mikolajczyk%2C+R">Rafael Mikolajczyk</a>, <a href="/search/q-bio?searchtype=author&query=Cattuto%2C+C">Ciro Cattuto</a>, <a href="/search/q-bio?searchtype=author&query=Kucharski%2C+A">Adam Kucharski</a>, <a href="/search/q-bio?searchtype=author&query=Riley%2C+S">Steven Riley</a>, <a href="/search/q-bio?searchtype=author&query=Kendall%2C+M">Michelle Kendall</a>, <a href="/search/q-bio?searchtype=author&query=Lythgoe%2C+K">Katrina Lythgoe</a>, <a href="/search/q-bio?searchtype=author&query=Abeler-D%C3%B6rner%2C+L">Lucie Abeler-D枚rner</a>, <a href="/search/q-bio?searchtype=author&query=Wymant%2C+C">Chris Wymant</a>, <a href="/search/q-bio?searchtype=author&query=Bonsall%2C+D">David Bonsall</a>, <a href="/search/q-bio?searchtype=author&query=Ferretti%2C+L">Luca Ferretti</a>, <a href="/search/q-bio?searchtype=author&query=Fraser%2C+C">Christophe Fraser</a> </p> <p class="abstract mathjax"> <span class="has-text-black-bis has-text-weight-semibold">Abstract</span>: <span class="abstract-short has-text-grey-dark mathjax" id="2102.05445v1-abstract-short" style="display: inline;"> Digital contact tracing is a public health intervention. It should be integrated with local health policy, provide rapid and accurate notifications to exposed individuals, and encourage high app uptake and adherence to quarantine. Real-time monitoring and evaluation of effectiveness of app-based contact tracing is key for improvement and public trust. </span> <span class="abstract-full has-text-grey-dark mathjax" id="2102.05445v1-abstract-full" style="display: none;"> Digital contact tracing is a public health intervention. It should be integrated with local health policy, provide rapid and accurate notifications to exposed individuals, and encourage high app uptake and adherence to quarantine. Real-time monitoring and evaluation of effectiveness of app-based contact tracing is key for improvement and public trust. <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2102.05445v1-abstract-full').style.display = 'none'; document.getElementById('2102.05445v1-abstract-short').style.display = 'inline';">△ Less</a> </span> </p> <p class="is-size-7"><span class="has-text-black-bis has-text-weight-semibold">Submitted</span> 10 February, 2021; <span class="has-text-black-bis has-text-weight-semibold">originally announced</span> February 2021. </p> <p class="comments is-size-7"> <span class="has-text-black-bis has-text-weight-semibold">Comments:</span> <span class="has-text-grey-dark mathjax">9 pages</span> </p> </li> <li class="arxiv-result"> <div class="is-marginless"> <p class="list-title is-inline-block"><a href="https://arxiv.org/abs/2004.11342">arXiv:2004.11342</a> <span> [<a href="https://arxiv.org/pdf/2004.11342">pdf</a>, <a href="https://arxiv.org/format/2004.11342">other</a>] </span> </p> <div class="tags is-inline-block"> <span class="tag is-small is-link tooltip is-tooltip-top" data-tooltip="Applications">stat.AP</span> <span class="tag is-small is-grey tooltip is-tooltip-top" data-tooltip="Populations and Evolution">q-bio.PE</span> <span class="tag is-small is-grey tooltip is-tooltip-top" data-tooltip="Methodology">stat.ME</span> </div> </div> <p class="title is-5 mathjax"> Estimating the number of infections and the impact of non-pharmaceutical interventions on COVID-19 in European countries: technical description update </p> <p class="authors"> <span class="search-hit">Authors:</span> <a href="/search/q-bio?searchtype=author&query=Flaxman%2C+S">Seth Flaxman</a>, <a href="/search/q-bio?searchtype=author&query=Mishra%2C+S">Swapnil Mishra</a>, <a href="/search/q-bio?searchtype=author&query=Gandy%2C+A">Axel Gandy</a>, <a href="/search/q-bio?searchtype=author&query=Unwin%2C+H+J+T">H Juliette T Unwin</a>, <a href="/search/q-bio?searchtype=author&query=Coupland%2C+H">Helen Coupland</a>, <a href="/search/q-bio?searchtype=author&query=Mellan%2C+T+A">Thomas A Mellan</a>, <a href="/search/q-bio?searchtype=author&query=Zhu%2C+H">Harrison Zhu</a>, <a href="/search/q-bio?searchtype=author&query=Berah%2C+T">Tresnia Berah</a>, <a href="/search/q-bio?searchtype=author&query=Eaton%2C+J+W">Jeffrey W Eaton</a>, <a href="/search/q-bio?searchtype=author&query=Guzman%2C+P+N+P">Pablo N P Guzman</a>, <a href="/search/q-bio?searchtype=author&query=Schmit%2C+N">Nora Schmit</a>, <a href="/search/q-bio?searchtype=author&query=Callizo%2C+L">Lucia Callizo</a>, <a href="/search/q-bio?searchtype=author&query=Team%2C+I+C+C+R">Imperial College COVID-19 Response Team</a>, <a href="/search/q-bio?searchtype=author&query=Whittaker%2C+C">Charles Whittaker</a>, <a href="/search/q-bio?searchtype=author&query=Winskill%2C+P">Peter Winskill</a>, <a href="/search/q-bio?searchtype=author&query=Xi%2C+X">Xiaoyue Xi</a>, <a href="/search/q-bio?searchtype=author&query=Ghani%2C+A">Azra Ghani</a>, <a href="/search/q-bio?searchtype=author&query=Donnelly%2C+C+A">Christl A. Donnelly</a>, <a href="/search/q-bio?searchtype=author&query=Riley%2C+S">Steven Riley</a>, <a href="/search/q-bio?searchtype=author&query=Okell%2C+L+C">Lucy C Okell</a>, <a href="/search/q-bio?searchtype=author&query=Vollmer%2C+M+A+C">Michaela A C Vollmer</a>, <a href="/search/q-bio?searchtype=author&query=Ferguson%2C+N+M">Neil M. Ferguson</a>, <a href="/search/q-bio?searchtype=author&query=Bhatt%2C+S">Samir Bhatt</a> </p> <p class="abstract mathjax"> <span class="has-text-black-bis has-text-weight-semibold">Abstract</span>: <span class="abstract-short has-text-grey-dark mathjax" id="2004.11342v1-abstract-short" style="display: inline;"> Following the emergence of a novel coronavirus (SARS-CoV-2) and its spread outside of China, Europe has experienced large epidemics. In response, many European countries have implemented unprecedented non-pharmaceutical interventions including case isolation, the closure of schools and universities, banning of mass gatherings and/or public events, and most recently, wide-scale social distancing in… <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2004.11342v1-abstract-full').style.display = 'inline'; document.getElementById('2004.11342v1-abstract-short').style.display = 'none';">▽ More</a> </span> <span class="abstract-full has-text-grey-dark mathjax" id="2004.11342v1-abstract-full" style="display: none;"> Following the emergence of a novel coronavirus (SARS-CoV-2) and its spread outside of China, Europe has experienced large epidemics. In response, many European countries have implemented unprecedented non-pharmaceutical interventions including case isolation, the closure of schools and universities, banning of mass gatherings and/or public events, and most recently, wide-scale social distancing including local and national lockdowns. In this technical update, we extend a semi-mechanistic Bayesian hierarchical model that infers the impact of these interventions and estimates the number of infections over time. Our methods assume that changes in the reproductive number - a measure of transmission - are an immediate response to these interventions being implemented rather than broader gradual changes in behaviour. Our model estimates these changes by calculating backwards from temporal data on observed to estimate the number of infections and rate of transmission that occurred several weeks prior, allowing for a probabilistic time lag between infection and death. In this update we extend our original model [Flaxman, Mishra, Gandy et al 2020, Report #13, Imperial College London] to include (a) population saturation effects, (b) prior uncertainty on the infection fatality ratio, (c) a more balanced prior on intervention effects and (d) partial pooling of the lockdown intervention covariate. We also (e) included another 3 countries (Greece, the Netherlands and Portugal). The model code is available at https://github.com/ImperialCollegeLondon/covid19model/ We are now reporting the results of our updated model online at https://mrc-ide.github.io/covid19estimates/ We estimated parameters jointly for all M=14 countries in a single hierarchical model. Inference is performed in the probabilistic programming language Stan using an adaptive Hamiltonian Monte Carlo (HMC) sampler. <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2004.11342v1-abstract-full').style.display = 'none'; document.getElementById('2004.11342v1-abstract-short').style.display = 'inline';">△ Less</a> </span> </p> <p class="is-size-7"><span class="has-text-black-bis has-text-weight-semibold">Submitted</span> 23 April, 2020; <span class="has-text-black-bis has-text-weight-semibold">originally announced</span> April 2020. </p> </li> <li class="arxiv-result"> <div class="is-marginless"> <p class="list-title is-inline-block"><a href="https://arxiv.org/abs/1903.08054">arXiv:1903.08054</a> <span> [<a href="https://arxiv.org/pdf/1903.08054">pdf</a>, <a href="https://arxiv.org/format/1903.08054">other</a>] </span> </p> <div class="tags is-inline-block"> <span class="tag is-small is-link tooltip is-tooltip-top" data-tooltip="Populations and Evolution">q-bio.PE</span> <span class="tag is-small is-grey tooltip is-tooltip-top" data-tooltip="Cell Behavior">q-bio.CB</span> </div> <div class="is-inline-block" style="margin-left: 0.5rem"> <div class="tags has-addons"> <span class="tag is-dark is-size-7">doi</span> <span class="tag is-light is-size-7"><a class="" href="https://doi.org/10.1016/j.epidem.2020.100406">10.1016/j.epidem.2020.100406 <i class="fa fa-external-link" aria-hidden="true"></i></a></span> </div> </div> </div> <p class="title is-5 mathjax"> Cellular reproduction number, generation time and growth rate differ between human- and avian-adapted influenza strains </p> <p class="authors"> <span class="search-hit">Authors:</span> <a href="/search/q-bio?searchtype=author&query=Yan%2C+A+W+C">Ada W. C. Yan</a>, <a href="/search/q-bio?searchtype=author&query=Zhou%2C+J">Jie Zhou</a>, <a href="/search/q-bio?searchtype=author&query=Beauchemin%2C+C+A+A">Catherine A. A. Beauchemin</a>, <a href="/search/q-bio?searchtype=author&query=Russell%2C+C+A">Colin A. Russell</a>, <a href="/search/q-bio?searchtype=author&query=Barclay%2C+W+S">Wendy S. Barclay</a>, <a href="/search/q-bio?searchtype=author&query=Riley%2C+S">Steven Riley</a> </p> <p class="abstract mathjax"> <span class="has-text-black-bis has-text-weight-semibold">Abstract</span>: <span class="abstract-short has-text-grey-dark mathjax" id="1903.08054v1-abstract-short" style="display: inline;"> When analysing in vitro data, growth kinetics of influenza strains are often compared by computing their growth rates, which are sometimes used as proxies for fitness. However, analogous to mechanistic epidemic models, the growth rate can be defined as a function of two parameters: the basic reproduction number (the average number of cells each infected cell infects) and the mean generation time (… <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('1903.08054v1-abstract-full').style.display = 'inline'; document.getElementById('1903.08054v1-abstract-short').style.display = 'none';">▽ More</a> </span> <span class="abstract-full has-text-grey-dark mathjax" id="1903.08054v1-abstract-full" style="display: none;"> When analysing in vitro data, growth kinetics of influenza strains are often compared by computing their growth rates, which are sometimes used as proxies for fitness. However, analogous to mechanistic epidemic models, the growth rate can be defined as a function of two parameters: the basic reproduction number (the average number of cells each infected cell infects) and the mean generation time (the average length of a replication cycle). Using a mechanistic model, previously published data from experiments in human lung cells, and newly generated data, we compared estimates of all three parameters for six influenza A strains. Using previously published data, we found that the two human-adapted strains (pre-2009 seasonal H1N1, and pandemic H1N1) had a lower basic reproduction number, shorter mean generation time and slower growth rate than the two avian-adapted strains (H5N1 and H7N9). These same differences were then observed in data from new experiments where two strains were engineered to have different internal proteins (pandemic H1N1 and H5N1), but the same surface proteins (PR8), confirming our initial findings and implying that differences between strains were driven by internal genes. Also, the model predicted that the human-adapted strains underwent more replication cycles than the avian-adapted strains by the time of peak viral load, potentially accumulating mutations more quickly. These results suggest that the in vitro reproduction number, generation time and growth rate differ between human-adapted and avian-adapted influenza strains, and thus could be used to assess host adaptation of internal proteins to inform pandemic risk assessment. <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('1903.08054v1-abstract-full').style.display = 'none'; document.getElementById('1903.08054v1-abstract-short').style.display = 'inline';">△ Less</a> </span> </p> <p class="is-size-7"><span class="has-text-black-bis has-text-weight-semibold">Submitted</span> 19 March, 2019; <span class="has-text-black-bis has-text-weight-semibold">originally announced</span> March 2019. </p> <p class="comments is-size-7"> <span class="has-text-black-bis has-text-weight-semibold">Comments:</span> <span class="has-text-grey-dark mathjax">24 pages, 5 figures, 8 supplementary figures, 1 supplementary table</span> </p> <p class="comments is-size-7"> <span class="has-text-black-bis has-text-weight-semibold">Report number:</span> RIKEN-iTHEMS-Report-19 <span class="has-text-black-bis has-text-weight-semibold">MSC Class:</span> 92C60; 92D15; 92D30 </p> <p class="comments is-size-7"> <span class="has-text-black-bis has-text-weight-semibold">Journal ref:</span> Epidemics, 33, Dec. (2020) 100406 </p> </li> <li class="arxiv-result"> <div class="is-marginless"> <p class="list-title is-inline-block"><a href="https://arxiv.org/abs/1308.4245">arXiv:1308.4245</a> <span> [<a href="https://arxiv.org/pdf/1308.4245">pdf</a>] </span> </p> <div class="tags is-inline-block"> <span class="tag is-small is-link tooltip is-tooltip-top" data-tooltip="Neurons and Cognition">q-bio.NC</span> </div> </div> <p class="title is-5 mathjax"> Evidence that Threatening Situations Enhance Creativity </p> <p class="authors"> <span class="search-hit">Authors:</span> <a href="/search/q-bio?searchtype=author&query=Riley%2C+S+N">Sean N. Riley</a>, <a href="/search/q-bio?searchtype=author&query=Gabora%2C+L">Liane Gabora</a> </p> <p class="abstract mathjax"> <span class="has-text-black-bis has-text-weight-semibold">Abstract</span>: <span class="abstract-short has-text-grey-dark mathjax" id="1308.4245v3-abstract-short" style="display: inline;"> We tested the hypothesis that threatening situations enhance creativity. 60 participants viewed a series of photographs and rated them on level of threat. They then wrote two short stories: one based on the photograph they rated as most threatening, and the other based on the photograph they rated as least threatening. The stories were rated for level of creativity. Paired samples t-tests revealed… <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('1308.4245v3-abstract-full').style.display = 'inline'; document.getElementById('1308.4245v3-abstract-short').style.display = 'none';">▽ More</a> </span> <span class="abstract-full has-text-grey-dark mathjax" id="1308.4245v3-abstract-full" style="display: none;"> We tested the hypothesis that threatening situations enhance creativity. 60 participants viewed a series of photographs and rated them on level of threat. They then wrote two short stories: one based on the photograph they rated as most threatening, and the other based on the photograph they rated as least threatening. The stories were rated for level of creativity. Paired samples t-tests revealed that stories based on threatening pictures produced a higher degree of creativity than those based on non-threatening pictures. Theoretical frameworks consistent with these findings are discussed. <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('1308.4245v3-abstract-full').style.display = 'none'; document.getElementById('1308.4245v3-abstract-short').style.display = 'inline';">△ Less</a> </span> </p> <p class="is-size-7"><span class="has-text-black-bis has-text-weight-semibold">Submitted</span> 9 July, 2019; <span class="has-text-black-bis has-text-weight-semibold">v1</span> submitted 20 August, 2013; <span class="has-text-black-bis has-text-weight-semibold">originally announced</span> August 2013. </p> <p class="comments is-size-7"> <span class="has-text-black-bis has-text-weight-semibold">Journal ref:</span> Proceedings of the 34th Annual Meeting of the Cognitive Science Society (pp. 2234-2239). Austin, TX: Cognitive Science Society. (2012) </p> </li> </ol> <div class="is-hidden-tablet">  <span class="help" style="display: inline-block;"><a href="https://github.com/arXiv/arxiv-search/releases">Search v0.5.6 released 2020-02-24</a>  </span> </div> </div> </main> <footer> <div class="columns is-desktop" role="navigation" aria-label="Secondary">  <div class="column"> <div class="columns"> <div class="column"> <ul class="nav-spaced"> <li><a href="https://info.arxiv.org/about">About</a></li> <li><a href="https://info.arxiv.org/help">Help</a></li> </ul> </div> <div class="column"> <ul class="nav-spaced"> <li> <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 512 512" class="icon filter-black" role="presentation"><title>contact arXiv</title><desc>Click here to contact arXiv</desc><path d="M502.3 190.8c3.9-3.1 9.7-.2 9.7 4.7V400c0 26.5-21.5 48-48 48H48c-26.5 0-48-21.5-48-48V195.6c0-5 5.7-7.8 9.7-4.7 22.4 17.4 52.1 39.5 154.1 113.6 21.1 15.4 56.7 47.8 92.2 47.6 35.7.3 72-32.8 92.3-47.6 102-74.1 131.6-96.3 154-113.7zM256 320c23.2.4 56.6-29.2 73.4-41.4 132.7-96.3 142.8-104.7 173.4-128.7 5.8-4.5 9.2-11.5 9.2-18.9v-19c0-26.5-21.5-48-48-48H48C21.5 64 0 85.5 0 112v19c0 7.4 3.4 14.3 9.2 18.9 30.6 23.9 40.7 32.4 173.4 128.7 16.8 12.2 50.2 41.8 73.4 41.4z"/></svg> <a href="https://info.arxiv.org/help/contact.html"> Contact</a> </li> <li> <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 512 512" class="icon filter-black" role="presentation"><title>subscribe to arXiv mailings</title><desc>Click here to subscribe</desc><path d="M476 3.2L12.5 270.6c-18.1 10.4-15.8 35.6 2.2 43.2L121 358.4l287.3-253.2c5.5-4.9 13.3 2.6 8.6 8.3L176 407v80.5c0 23.6 28.5 32.9 42.5 15.8L282 426l124.6 52.2c14.2 6 30.4-2.9 33-18.2l72-432C515 7.8 493.3-6.8 476 3.2z"/></svg> <a href="https://info.arxiv.org/help/subscribe"> Subscribe</a> </li> </ul> </div> </div> </div>   <div class="column"> <div class="columns"> <div class="column"> <ul class="nav-spaced"> <li><a href="https://info.arxiv.org/help/license/index.html">Copyright</a></li> <li><a href="https://info.arxiv.org/help/policies/privacy_policy.html">Privacy Policy</a></li> </ul> </div> <div class="column sorry-app-links"> <ul class="nav-spaced"> <li><a href="https://info.arxiv.org/help/web_accessibility.html">Web Accessibility Assistance</a></li> <li> <p class="help"> <a class="a11y-main-link" href="https://status.arxiv.org" target="_blank">arXiv Operational Status <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 256 512" class="icon filter-dark_grey" role="presentation"><path d="M224.3 273l-136 136c-9.4 9.4-24.6 9.4-33.9 0l-22.6-22.6c-9.4-9.4-9.4-24.6 0-33.9l96.4-96.4-96.4-96.4c-9.4-9.4-9.4-24.6 0-33.9L54.3 103c9.4-9.4 24.6-9.4 33.9 0l136 136c9.5 9.4 9.5 24.6.1 34z"/></svg></a><br> Get status notifications via <a class="is-link" href="https://subscribe.sorryapp.com/24846f03/email/new" target="_blank"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 512 512" class="icon filter-black" role="presentation"><path d="M502.3 190.8c3.9-3.1 9.7-.2 9.7 4.7V400c0 26.5-21.5 48-48 48H48c-26.5 0-48-21.5-48-48V195.6c0-5 5.7-7.8 9.7-4.7 22.4 17.4 52.1 39.5 154.1 113.6 21.1 15.4 56.7 47.8 92.2 47.6 35.7.3 72-32.8 92.3-47.6 102-74.1 131.6-96.3 154-113.7zM256 320c23.2.4 56.6-29.2 73.4-41.4 132.7-96.3 142.8-104.7 173.4-128.7 5.8-4.5 9.2-11.5 9.2-18.9v-19c0-26.5-21.5-48-48-48H48C21.5 64 0 85.5 0 112v19c0 7.4 3.4 14.3 9.2 18.9 30.6 23.9 40.7 32.4 173.4 128.7 16.8 12.2 50.2 41.8 73.4 41.4z"/></svg>email</a> or <a class="is-link" href="https://subscribe.sorryapp.com/24846f03/slack/new" target="_blank"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512" class="icon filter-black" role="presentation"><path d="M94.12 315.1c0 25.9-21.16 47.06-47.06 47.06S0 341 0 315.1c0-25.9 21.16-47.06 47.06-47.06h47.06v47.06zm23.72 0c0-25.9 21.16-47.06 47.06-47.06s47.06 21.16 47.06 47.06v117.84c0 25.9-21.16 47.06-47.06 47.06s-47.06-21.16-47.06-47.06V315.1zm47.06-188.98c-25.9 0-47.06-21.16-47.06-47.06S139 32 164.9 32s47.06 21.16 47.06 47.06v47.06H164.9zm0 23.72c25.9 0 47.06 21.16 47.06 47.06s-21.16 47.06-47.06 47.06H47.06C21.16 243.96 0 222.8 0 196.9s21.16-47.06 47.06-47.06H164.9zm188.98 47.06c0-25.9 21.16-47.06 47.06-47.06 25.9 0 47.06 21.16 47.06 47.06s-21.16 47.06-47.06 47.06h-47.06V196.9zm-23.72 0c0 25.9-21.16 47.06-47.06 47.06-25.9 0-47.06-21.16-47.06-47.06V79.06c0-25.9 21.16-47.06 47.06-47.06 25.9 0 47.06 21.16 47.06 47.06V196.9zM283.1 385.88c25.9 0 47.06 21.16 47.06 47.06 0 25.9-21.16 47.06-47.06 47.06-25.9 0-47.06-21.16-47.06-47.06v-47.06h47.06zm0-23.72c-25.9 0-47.06-21.16-47.06-47.06 0-25.9 21.16-47.06 47.06-47.06h117.84c25.9 0 47.06 21.16 47.06 47.06 0 25.9-21.16 47.06-47.06 47.06H283.1z"/></svg>slack</a> </p> </li> </ul> </div> </div> </div>  </div> </footer> <script src="https://static.arxiv.org/static/base/1.0.0a5/js/member_acknowledgement.js"></script> </body> </html>

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