scholarly journals Inferring the number of COVID-19 cases from recently reported deaths

2020 ◽  
Author(s):  
Thibaut Jombart ◽  
Kevin van Zandvoort ◽  
Timothy W Russell ◽  
Christopher I Jarvis ◽  
Amy Gimma ◽  
...  
Keyword(s):  
Contact Tracing ◽  
Online Tool ◽  
Response Strategies ◽  
User Friendly

ABSTRACTWe estimate the number of COVID-19 cases from newly reported deaths in a population without previous reports. Our results suggest that by the time a single death occurs, hundreds to thousands of cases are likely to be present in that population. This suggests containment via contact tracing will be challenging at this point, and other response strategies should be considered. Our approach is implemented in a publicly available, user-friendly, online tool.

scholarly journals Inferring the number of COVID-19 cases from recently reported deaths

2020 ◽  
Vol 5 ◽  
pp. 78 ◽  
Author(s):  
Thibaut Jombart ◽  
Kevin van Zandvoort ◽  
Timothy W. Russell ◽  
Christopher I. Jarvis ◽  
Amy Gimma ◽  
...  
Keyword(s):  
Contact Tracing ◽  
Online Tool ◽  
Response Strategies ◽  
User Friendly

We estimate the number of COVID-19 cases from newly reported deaths in a population without previous reports. Our results suggest that by the time a single death occurs, hundreds to thousands of cases are likely to be present in that population. This suggests containment via contact tracing will be challenging at this point, and other response strategies should be considered. Our approach is implemented in a publicly available, user-friendly, online tool.

scholarly journals Uncovering two phases of early intercontinental COVID-19 transmission dynamics

2020 ◽  
Vol 27 (8) ◽  
Author(s):  
Jing Yang ◽  
Juan Li ◽  
Shengjie Lai ◽  
Corrine W Ruktanonchai ◽  
Weijia Xing ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
International Travel ◽  
Contact Tracing ◽  
Genetic Sequencing ◽  
Response Strategies ◽  
The World ◽  
Containment Measures ◽  
The Usa ◽  
Community Transmission ◽  
Two Phases

Abstract Background The COVID-19 pandemic has posed an ongoing global crisis, but how the virus spread across the world remains poorly understood. This is of vital importance for informing current and future pandemic response strategies. Methods We performed two independent analyses, travel network-based epidemiological modelling and Bayesian phylogeographic inference, to investigate the intercontinental spread of COVID-19. Results Both approaches revealed two distinct phases of COVID-19 spread by the end of March 2020. In the first phase, COVID-19 largely circulated in China during mid-to-late January 2020 and was interrupted by containment measures in China. In the second and predominant phase extending from late February to mid-March, unrestricted movements between countries outside of China facilitated intercontinental spread, with Europe as a major source. Phylogenetic analyses also revealed that the dominant strains circulating in the USA were introduced from Europe. However, stringent restrictions on international travel across the world since late March have substantially reduced intercontinental transmission. Conclusions Our analyses highlight that heterogeneities in international travel have shaped the spatiotemporal characteristics of the pandemic. Unrestricted travel caused a large number of COVID-19 exportations from Europe to other continents between late February and mid-March, which facilitated the COVID-19 pandemic. Targeted restrictions on international travel from countries with widespread community transmission, together with improved capacity in testing, genetic sequencing and contact tracing, can inform timely strategies for mitigating and containing ongoing and future waves of COVID-19 pandemic.

scholarly journals VIP-HL: Semi-automated ACMG/AMP variant interpretation platform for genetic hearing loss

2020 ◽  
Author(s):  
Jiguang Peng ◽  
Jiale Xiang ◽  
Xiangqian Jin ◽  
Junhua Meng ◽  
Nana Song ◽  
...  
Keyword(s):  
Hearing Loss ◽  
Expert Panel ◽  
Sequence Variant ◽  
Variant Interpretation ◽  
Web Interface ◽  
Online Tool ◽  
Genetic Hearing Loss ◽  
Genetics And Genomics ◽  
Evidence Based Guidelines ◽  
User Friendly

The American College of Medical Genetics and Genomics, and the Association for Molecular Pathology (ACMG/AMP) have proposed a set of evidence-based guidelines to support sequence variant interpretation. The ClinGen hearing loss expert panel (HL-EP) introduced further specifications into the ACMG/AMP framework for genetic hearing loss. This study developed a tool named VIP-HL, aiming to semi-automate the HL ACMG/AMP rules. VIP-HL aggregates information from external databases to automate 13 out of 24 ACMG/AMP rules specified by HL-EP, namely PVS1, PS1, PM1, PM2, PM4, PM5, PP3, BA1, BS1, BS2, BP3, BP4, and BP7. We benchmarked VIP-HL using 50 variants where 83 rules were activated by the ClinGen HL-EP. VIP-HL concordantly activated 96% (80/83) rules, significantly higher than that of by InterVar (47%; 39/83). Of 4948 ClinVar star 2+ variants from 142 deafness-related genes, VIP-HL achieved an overall variant interpretation concordance in 88.0% (4353/4948). VIP-HL is an integrated online tool for reliable automated variant classification in hearing loss genes. It assists curators in variant interpretation and provides a platform for users to share classifications with each other. VIP-HL is available with a user-friendly web interface at http://hearing.genetics.bgi.com/.

A COOPERATIVE APPROACH TO OIL SPILL PLANNING

1995 ◽  
Vol 1995 (1) ◽  
pp. 921-922
Author(s):  
William Gorham ◽  
Martin Cramer
Keyword(s):  
Information System ◽  
Geographic Information System ◽  
Oil Spill ◽  
Geographic Information ◽  
Marine Resources ◽  
Resource Manual ◽  
Response Strategies ◽  
Cooperative Approach ◽  
Vessel Response ◽  
User Friendly

ABSTRACT California's oil spill cooperatives joined forces to prepare a regional resource manual. The manual provided cooperative members detailed information on sensitive marine resources, response strategies, spill envelopes, response resources, navigation hazards, and other topics for incorporation into individual facility or vessel response plans being prepared for compliance with the stringent requirements of California's Oil Spill Prevention and Response Act. Detailed maps of sensitive resources, response strategies, and spill envelopes were prepared using a geographic information system (GIS) for ease of presentation and revision. Maps were supported by detailed tables on the facing page, producing a maximally user-friendly document.

scholarly journals Dynamical SPQEIR model assesses the effectiveness of non-pharmaceutical interventions against COVID-19 epidemic outbreaks

2020 ◽  
Author(s):  
Daniele Proverbio ◽  
Françoise Kemp ◽  
Stefano Magni ◽  
Andreas Husch ◽  
Atte Aalto ◽  
...  
Keyword(s):  
Decision Makers ◽  
Contact Tracing ◽  
Online Tool ◽  
Seir Model ◽  
Social Distancing ◽  
Quantitative Understanding ◽  
Cross Country ◽  
Pharmaceutical Interventions

AbstractAgainst the current COVID-19 pandemic, governments worldwide have devised a variety of non-pharmaceutical interventions to suppress it, but the efficacy of distinct measures is not yet well quantified. In this paper, we propose a novel tool to achieve this quantification. In fact, this paper develops a new extended epidemic SEIR model, informed by a socio-political classification of different interventions, to assess the value of several suppression approaches. First, we inquire the conceptual effect of suppression parameters on the infection curve. Then, we illustrate the potential of our model on data from a number of countries, to perform cross-country comparisons. This gives information on the best synergies of interventions to control epidemic outbreaks while minimising impact on socio-economic needs. For instance, our results suggest that, while rapid and strong lock-down is an effective pandemic suppression measure, a combination of social distancing and contact tracing can achieve similar suppression synergistically. This quantitative understanding will support the establishment of mid- and long-term interventions, to prepare containment strategies against further outbreaks. This paper also provides an online tool that allows researchers and decision makers to interactively simulate diverse scenarios with our model.

TDAview: an online visualization tool for topological data analysis

2020 ◽  
Vol 36 (18) ◽  
pp. 4805-4809
Author(s):  
Kieran Walsh ◽  
Mircea A Voineagu ◽  
Fatemeh Vafaee ◽  
Irina Voineagu
Keyword(s):  
Data Analysis ◽  
Open Source Software ◽  
Topological Data Analysis ◽  
Graph Visualization ◽  
Online Tool ◽  
Wide Range ◽  
Data Points ◽  
Programming Knowledge ◽  
User Friendly ◽  
Topological Data

Abstract Summary TDAview is an online tool for topological data analysis (TDA) and visualization. It implements the Mapper algorithm for TDA and provides extensive graph visualization options. TDAview is a user-friendly tool that allows biologists and clinicians without programming knowledge to harness the power of TDA. TDAview supports an analysis and visualization mode in which a Mapper graph is constructed based on user-specified parameters, followed by graph visualization. It can also be used in a visualization only mode in which TDAview is used for visualizing the data properties of a Mapper graph generated using other open-source software. The graph visualization options allow data exploration by graphical display of metadata variable values for nodes and edges, as well as the generation of publishable figures. TDAview can handle large datasets, with tens of thousands of data points, and thus has a wide range of applications for high-dimensional data, including the construction of topology-based gene co-expression networks. Availability and implementation TDAview is a free online tool available at https://voineagulab.github.io/TDAview/. The source code, usage documentation and example data are available at TDAview GitHub repository: https://github.com/Voineagulab/TDAview.

scholarly journals California's Response to USCG Nationwide Standardization of Area Contingency Plans

2021 ◽  
Vol 2021 (1) ◽  
Author(s):  
Cassidee Shinn
Keyword(s):  
Los Angeles ◽  
The United States ◽  
Lessons Learned ◽  
Coast Guard ◽  
Response Strategy ◽  
California Department ◽  
Response Strategies ◽  
Contingency Plans ◽  
Sensitive Site ◽  
User Friendly

ABSTRACT California Department of Fish and Wildlife (CDFW) - Office of Spill Prevention and Response (OSPR), working with the United States Coast Guard (USCG), and Area Committee members, made significant strides to streamline the Area Contingency Plans (ACPs) for improved efficiency and statewide consistency to adhere to new USCG guidance. Beginning with Sector San Diego's ACP, which underwent major revision in 2018, and Sector Los Angeles/Long Beach in 2019, OSPR worked closely with USCG to ensure that there is comparable information statewide, improved maps and GIS compatibility, and updated environmentally and economically sensitive site information. OSPR created a new environmental sensitive site database, including more user-friendly Geographic Response Strategy pages for those identified sites. OSPR also revised the content of Section 9800, which describes the environmental, cultural, historic, and economic sensitivities of a given ACP area, and includes the Geographic Response Strategies. This paper describes in detail the contributions and changes that OSPR has made to California ACPs since 2018. It highlights its approaches to streamlining for efficiency and statewide consistency and lessons learned from the new revision and approval processes.

scholarly journals MeltingPlot: a user-friendly online tool for epidemiological investigation using High Resolution Melting data

2020 ◽  
Author(s):  
Matteo Perini ◽  
Gherard Batisti Biffignandi ◽  
Domenico Di Carlo ◽  
Ajay Ratan Pasala ◽  
Aurora Piazza ◽  
...  
Keyword(s):  
High Resolution ◽  
High Resolution Melting ◽  
Epidemiological Studies ◽  
Supplementary Information ◽  
Web Interface ◽  
Web Tool ◽  
Online Tool ◽  
Link Type ◽  
Surveillance Programs ◽  
User Friendly

AbstractSummaryMeltingPlot is an open source web tool for pathogen typing and epidemiological investigations using High Resolution Melting (HRM) data. The tool implements a graph-based algorithm designed to discriminate pathogen clones on the basis of HRM data, producing portable typing results. MeltingPlot also merges typing information with isolates and patients metadata to create graphical and tabular outputs useful in epidemiological studies. HRM technique allows pathogen typing in less than 5 hours with ~5 euros per sample. MeltingPlot is the first tool specifically designed for HRM-based epidemiological studies and it can analyse hundreds of isolates in a few seconds. Thus, the use of MeltingPlot makes HRM-based typing suitable for large surveillance programs as well as for rapid outbreak reconstructions.Availability and implementationMeltingPlot is implemented in R.The web interface is available at https://skynet.unimi.it/index.php/tools/meltingplot.The source code is also available at https://github.com/MatteoPS/[email protected] informationSupplementary data are available at Bioinformatics online.

scholarly journals PAWER: Protein Array Web ExploreR

2019 ◽  
Author(s):  
Dmytro Fishman ◽  
Ivan Kuzmin ◽  
Priit Adler ◽  
Jaak Vilo ◽  
Hedi Peterson
Keyword(s):  
Protein Microarray ◽  
Differential Expression Analysis ◽  
R Package ◽  
Functional Enrichment ◽  
Activity Levels ◽  
Online Tool ◽  
Typical Data ◽  
Protein Microarray Analysis ◽  
User Friendly ◽  
Real Challenge

AbstractProtein microarray is a well-established approach for characterizing activity levels of thousands of proteins in a parallel manner. Analysis of protein microarray data is complex and time-consuming, while existing solutions are either outdated or challenging to use without programming skills. The typical data analysis pipeline consists of a data preprocessing step, followed by differential expression analysis, which is then put into context via functional enrichment. Normally, biologists would need to assemble their own workflow by combining a set of unrelated tools to analyze experimental data. Provided that most of these tools are developed independently by various bioinformatics groups, making them work together could be a real challenge. Here we present PAWER, the first online tool for protein microarray analysis. PAWER enables biologists to carry out all the necessary analysis steps in one go. PAWER provides access to state-of-the-art computational methods through a user-friendly interface, resulting in publication-ready illustrations. We also provide an R package for more advanced use cases, such as bespoke analysis workflows. PAWER is freely available at https://biit.cs.ut.ee/pawer.

scholarly journals Why lockdown? Simplified arithmetic tools for decision-makers, health professionals, journalists and the general public to explore containment options for the novel coronavirus

2020 ◽  
Author(s):  
Gerry F. Killeen ◽  
Samson S Kiware
Keyword(s):  
National Level ◽  
Epidemiological Surveillance ◽  
Contact Tracing ◽  
The Novel ◽  
Minimal Impact ◽  
High Incidence ◽  
United Republic Of Tanzania ◽  
Novel Coronavirus ◽  
User Friendly ◽  
Parameter Values

SummaryHalf the world’s population is already under lock-down and the remainder will have to follow if the ongoing novel coronavirus 2019 (COVID-19) virus pandemic is to be contained. Faced with such brutally difficult decisions, it is essential that as many people as possible understand (1) why lock-down interventions represent the only realistic way for individual countries to contain their national-level epidemics before they turn into public health catastrophes, (2) why these need to be implemented so early, so aggressively and for such extended periods, and (3) why international co-operation to conditionally re-open trade and travel between countries that have successfully eliminated local transmission represents the only way to contain the pandemic at global level. Here we present simplified arithmetic models of COVID-19 transmission, control and elimination in user-friendly Shiny and Excel formats that allow non-specialists to explore, query, critique and understand the containment decisions facing their country and the world at large. Based on parameter values representative of the United Republic of Tanzania, which is still early enough in its epidemic cycle and response to avert a national catastrophe, national containment and elimination with less than 10 deaths is predicted for highly rigorous lock down within 5 weeks of the first confirmed cases and maintained for 15 weeks. However, elimination may only be sustained if case importation from outside the country is comprehensively contained by isolating for three weeks all incoming travellers, except those from countries certified as COVID-free in the future. Any substantive relaxation of these assumptions, specifically shortening the lock-down period, less rigorous lock-down or imperfect importation containment, may facilitate epidemic re-initiation, resulting in over half a million deaths unless rigorously contained a second time. Removing contact tracing and isolation has minimal impact on successful containment trajectories because high incidence of similar mild symptoms caused by other common pathogens attenuates detection success of COVID-19 testing. Nevertheless, contact tracing is recommended as an invaluable epidemiological surveillance platform for monitoring and characterizing the epidemic, and for understanding the influence of interventions on transmission dynamics.

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