scholarly journals Improving COVID-19 Testing Efficiency using Guided Agglomerative Sampling

2020 ◽  
Author(s):  
Fayyaz Minhas ◽  
Dimitris Grammatopoulos ◽  
Lawrence Young ◽  
Imran Amin ◽  
David Snead ◽  
...  
Keyword(s):  
Large Scale ◽  
Resource Constraints ◽  
Large Population ◽  
Sampling Strategy ◽  
Population Surveillance ◽  
Large Scale Testing ◽  
Scale Population ◽  
Simulation Results ◽  
The Given ◽  
Test Outcomes

AbstractOne of the challenges in the current COVID-19 crisis is the time and cost of performing tests especially for large-scale population surveillance. Since, the probability of testing positive in large population studies is expected to be small (<15%), therefore, most of the test outcomes will be negative. Here, we propose the use of agglomerative sampling which can prune out multiple negative cases in a single test by intelligently combining samples from different individuals. The proposed scheme builds on the assumption that samples from the population may not be independent of each other. Our simulation results show that the proposed sampling strategy can significantly increase testing capacity under resource constraints: on average, a saving of ~40% tests can be expected assuming a positive test probability of 10% across the given samples. The proposed scheme can also be used in conjunction with heuristic or Machine Learning guided clustering for improving the efficiency of large-scale testing further. The code for generating the simulation results for this work is available here: https://github.com/foxtrotmike/AS.

scholarly journals STAMP: a multiplex sequencing method for simultaneous evaluation of mitochondrial DNA heteroplasmies and content

2020 ◽  
Author(s):  
Xiaoxian Guo ◽  
Yiqin Wang ◽  
Ruoyu Zhang ◽  
Zhenglong Gu
Keyword(s):  
Large Scale ◽  
Nuclear Dna ◽  
Large Population ◽  
High Sensitivity ◽  
Cost Effective ◽  
Cost Effective Method ◽  
Sequencing Method ◽  
Scale Population ◽  
Mtdna Variants ◽  
Multiplex Sequencing

ABSTRACTHuman mitochondrial genome (mtDNA) variations, such as mtDNA heteroplasmies (the co-existence of mutated and wild-type mtDNA), have received increasing attention in recent years for their clinical relevance to numerous diseases. But large-scale population studies of mtDNA heteroplasmies have been lagging due to the lack of a labor- and cost-effective method. Here, we present a novel human mtDNA sequencing method called STAMP (sequencing by targeted amplification of multiplex probes) for measuring mtDNA heteroplasmies and content in a streamlined workflow. We show that STAMP has high mapping rates to mtDNA, deep coverage of unique reads, and high tolerance to sequencing and PCR errors when applied to human samples. STAMP also has high sensitivity and low false positive rates in identifying artificial mtDNA variants at fractions as low as 0.5% in genomic DNA samples. We further extend STAMP, by including nuclear DNA-targeting probes, to enable assessment of relative mtDNA content in the same assay. The high cost-effectiveness of STAMP, along with the flexibility of using it for measuring various aspects of mtDNA variations, will accelerate the research of mtDNA heteroplasmies and content in large population cohorts, and in the context of human diseases and aging.

scholarly journals STAMP: a multiplex sequencing method for simultaneous evaluation of mitochondrial DNA heteroplasmies and content

2020 ◽  
Vol 2 (4) ◽  
Author(s):  
Xiaoxian Guo ◽  
Yiqin Wang ◽  
Ruoyu Zhang ◽  
Zhenglong Gu
Keyword(s):  
Large Scale ◽  
Nuclear Dna ◽  
Large Population ◽  
High Sensitivity ◽  
Cost Effective ◽  
Cost Effective Method ◽  
Sequencing Method ◽  
Scale Population ◽  
Mtdna Variants ◽  
Multiplex Sequencing

Abstract Human mitochondrial genome (mtDNA) variations, such as mtDNA heteroplasmies (the co-existence of mutated and wild-type mtDNA), have received increasing attention in recent years for their clinical relevance to numerous diseases. But large-scale population studies of mtDNA heteroplasmies have been lagging due to the lack of a labor- and cost-effective method. Here, we present a novel human mtDNA sequencing method called STAMP (sequencing by targeted amplification of multiplex probes) for measuring mtDNA heteroplasmies and content in a streamlined workflow. We show that STAMP has high-mapping rates to mtDNA, deep coverage of unique reads and high tolerance to sequencing and polymerase chain reaction errors when applied to human samples. STAMP also has high sensitivity and low false positive rates in identifying artificial mtDNA variants at fractions as low as 0.5% in genomic DNA samples. We further extend STAMP, by including nuclear DNA-targeting probes, to enable assessment of relative mtDNA content in the same assay. The high cost-effectiveness of STAMP, along with the flexibility of using it for measuring various aspects of mtDNA variations, will accelerate the research of mtDNA heteroplasmies and content in large population cohorts, and in the context of human diseases and aging.

scholarly journals Validation testing to determine the effectiveness of lateral flow testing for asymptomatic SARS-CoV-2 detection in low prevalence settings

2020 ◽  
Author(s):  
Jack Ferguson ◽  
Steven Dunn ◽  
Angus Best ◽  
Jeremy Mirza ◽  
Benita Percival ◽  
...  
Keyword(s):  
Large Scale ◽  
Care Home ◽  
Population Surveillance ◽  
Lateral Flow ◽  
The United Kingdom ◽  
Scale Population ◽  
Surveillance Programs ◽  
Low Prevalence ◽  
The University ◽  
Flow Devices

AbstractLateral flow devices are quickly being implemented for use in large scale population surveillance programs for SARS-CoV-2 infection in the United Kingdom. These programs have been piloted in city wide screening in the city of Liverpool, and are now being rolled out to support care home visits and the return home of University students for the Christmas break. Here we present data on the performance of Lateral Flow devices to test almost 8,000 students at the University of Birmingham between December 2nd and December 9th 2020. The performance is validated against almost 800 samples using PCR performed in the University Pillar 2 testing lab, and theoretically validated on thousands of Pillar 2 PCR testing results performed on low-prevalence care home testing samples. Our data shows that Lateral Flow Devices do not detect infections presenting with PCR Ct values over 29-30, meaning that only 3.2% (95% CI 0.6% to 15.6%) of total cases in the student population were detected, but that as many of 85% of cases tested in the Pillar 2 PCR lab would have been detected theoretically

Community-Driven Approach for Youth Health Survey Administration and Data Utilization

2020 ◽  
pp. 152483992091069
Author(s):  
Leonardo Kattari ◽  
Lauren Cikara ◽  
Ming Ma ◽  
Ashley Brooks-Russell
Keyword(s):  
Rural Communities ◽  
Large Scale ◽  
Population Surveillance ◽  
Surveillance Systems ◽  
Youth Survey ◽  
Effective Interventions ◽  
Strategic Approach ◽  
Scale Population ◽  
Survey Administration ◽  
State And Local

Large-scale population surveillance systems may fall short in capturing localized data specifically from rural communities. A three-tiered engagement approach is implemented by survey administrators that focuses on supporting communities and schools to better understand the health of youth locally and identify the most effective interventions. This community-driven approach to survey administration addresses the locality gap and evolves a statewide youth survey to better meet the needs of the state and local communities, as well as alleviates survey burden in schools through a unified, strategic approach.

scholarly journals Validation testing to determine the sensitivity of lateral flow testing for asymptomatic SARS-CoV-2 detection in low prevalence settings: Testing frequency and public health messaging is key

PLoS Biology ◽  
2021 ◽  
Vol 19 (4) ◽  
pp. e3001216
Author(s):  
Jack Ferguson ◽  
Steven Dunn ◽  
Angus Best ◽  
Jeremy Mirza ◽  
Benita Percival ◽  
...  
Keyword(s):  
Large Scale ◽  
Care Home ◽  
Population Surveillance ◽  
Lateral Flow ◽  
The United Kingdom ◽  
Testing Frequency ◽  
Scale Population ◽  
Surveillance Programs ◽  
Low Prevalence ◽  
The University

Lateral flow devices (LFDs) are quickly being implemented for use in large-scale population surveillance programs for SARS-CoV-2 infection in the United Kingdom. These programs have been piloted in city-wide screening in the city of Liverpool and are now being rolled out to support care home visits and the return home of University students for the Christmas break. Here, we present data on the performance of LFDs to test almost 8,000 students at the University of Birmingham between December 2 and December 9, 2020. The performance is validated against almost 800 samples using PCR performed in the University Pillar 2 testing lab and theoretically validated on thousands of Pillar 2 PCR testing results performed on low-prevalence care home testing samples. Our data show that LFDs do not detect infections presenting with PCR Ct values over 29 to 30 as determined using the Thermo Fisher TaqPath asssay. This may be of particular importance in detecting individuals that are either at the early, or late stages of infection, and reinforces the need for frequent, recurrent testing.

scholarly journals Publisher Correction: A link between appendectomy and gastrointestinal cancers: a large-scale population-based cohort study in Korea

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Youn Young Park ◽  
Kil‑yong Lee ◽  
Seong Taek Oh ◽  
Sang Hyun Park ◽  
Kyung Do Han ◽  
...  
Keyword(s):  
Cohort Study ◽  
Large Scale ◽  
Population Based ◽  
Gastrointestinal Cancers ◽  
Scale Population

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

scholarly journals Design and Evaluation of Large-Scale IoT-Enabled Healthcare Architecture

2021 ◽  
Vol 11 (8) ◽  
pp. 3623
Author(s):  
Omar Said ◽  
Amr Tolba
Keyword(s):  
Packet Loss ◽  
Large Scale ◽  
Performance Metrics ◽  
Medical System ◽  
Healthcare Data ◽  
High Altitude Platforms ◽  
Wide Range ◽  
Simulation Results ◽  
Healthcare Architecture ◽  
The Internet Of Things

Employment of the Internet of Things (IoT) technology in the healthcare field can contribute to recruiting heterogeneous medical devices and creating smart cooperation between them. This cooperation leads to an increase in the efficiency of the entire medical system, thus accelerating the diagnosis and curing of patients, in general, and rescuing critical cases in particular. In this paper, a large-scale IoT-enabled healthcare architecture is proposed. To achieve a wide range of communication between healthcare devices, not only are Internet coverage tools utilized but also satellites and high-altitude platforms (HAPs). In addition, the clustering idea is applied in the proposed architecture to facilitate its management. Moreover, healthcare data are prioritized into several levels of importance. Finally, NS3 is used to measure the performance of the proposed IoT-enabled healthcare architecture. The performance metrics are delay, energy consumption, packet loss, coverage tool usage, throughput, percentage of served users, and percentage of each exchanged data type. The simulation results demonstrate that the proposed IoT-enabled healthcare architecture outperforms the traditional healthcare architecture.

scholarly journals Using Bus Ticketing Big Data to Investigate the Behaviors of the Population Flow of Chinese Suburban Residents in the Post-COVID-19 Phase

2021 ◽  
Vol 18 (11) ◽  
pp. 6066
Author(s):  
Yanbing Bai ◽  
Lu Sun ◽  
Haoyu Liu ◽  
Chao Xie
Keyword(s):  
Travel Behavior ◽  
Large Scale ◽  
Behavior Patterns ◽  
Population Movements ◽  
Economic Level ◽  
Passenger Travel ◽  
Scale Population ◽  
Travel Behaviors ◽  
Railway Passenger ◽  
And Control

Large-scale population movements can turn local diseases into widespread epidemics. Grasping the characteristic of the population flow in the context of the COVID-19 is of great significance for providing information to epidemiology and formulating scientific and reasonable prevention and control policies. Especially in the post-COVID-19 phase, it is essential to maintain the achievement of the fight against the epidemic. Previous research focuses on flight and railway passenger travel behavior and patterns, but China also has numerous suburban residents with a not-high economic level; investigating their travel behaviors is significant for national stability. However, estimating the impacts of the COVID-19 for suburban residents’ travel behaviors remains challenging because of lacking apposite data. Here we submit bus ticketing data including approximately 26,000,000 records from April 2020–August 2020 for 2705 stations. Our results indicate that Suburban residents in Chinese Southern regions are more likely to travel by bus, and travel frequency is higher. Associated with the economic level, we find that residents in the economically developed region more likely to travel or carry out various social activities. Considering from the perspective of the traveling crowd, we find that men and young people are easier to travel by bus; however, they are exactly the main workforce. The indication of our findings is that suburban residents’ travel behavior is affected profoundly by economy and consistent with the inherent behavior patterns before the COVID-19 outbreak. We use typical regions as verification and it is indeed the case.

scholarly journals The Flexible Operation of Coal Power and Its Renewable Integration Potential in China

2019 ◽  
Vol 11 (16) ◽  
pp. 4424 ◽  
Author(s):  
Chunning Na ◽  
Huan Pan ◽  
Yuhong Zhu ◽  
Jiahai Yuan ◽  
Lixia Ding ◽  
...  
Keyword(s):  
Renewable Energy ◽  
Power Systems ◽  
Power System ◽  
Large Scale ◽  
Renewable Integration ◽  
Flexible Resources ◽  
Feasible Option ◽  
Coal Power ◽  
Simulation Results ◽  
Flexible Operation

At present time, China’s power systems face significant challenges in integrating large-scale renewable energy and reducing the curtailed renewable energy. In order to avoid the curtailment of renewable energy, the power systems need significant flexibility requirements in China. In regions where coal is still heavily relied upon for generating electricity, the flexible operations of coal power units will be the most feasible option to face these challenges. The study first focused on the reasons why the flexible operation of existing coal power units would potentially promote the integration of renewable energy in China and then reviewed the impacts on the performance levels of the units. A simple flexibility operation model was constructed to estimate the integration potential with the existing coal power units under several different scenarios. This study’s simulation results revealed that the existing retrofitted coal power units could provide flexibility in the promotion of the integration of renewable energy in a certain extent. However, the integration potential increment of 20% of the rated power for the coal power units was found to be lower than that of 30% of the rated power. Therefore, by considering the performance impacts of the coal power units with low performances in load operations, it was considered to not be economical for those units to operate at lower than 30% of the rated power. It was believed that once the capacity share of the renewable energy had achieved a continuously growing trend, the existing coal power units would fail to meet the flexibility requirements. Therefore, it was recommended in this study that other flexible resources should be deployed in the power systems for the purpose of reducing the curtailment of renewable energy. Furthermore, based on this study’s obtained evidence, in order to realize a power system with high proportions of renewable energy, China should strive to establish a power system with adequate flexible resources in the future.

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