scholarly journals Validation of a rapid and sensitive SARS-CoV-2 screening system developed for pandemic-scale infection surveillance

2021 ◽  
Author(s):  
Robert Dewhurst ◽  
Tatjana Heinrich ◽  
Paul Watt ◽  
Paul Ostergaard ◽  
Jose Maria Marimon ◽  
...  
Keyword(s):  
Large Scale ◽  
Vaccine Coverage ◽  
Rapid Identification ◽  
Sentinel Surveillance ◽  
Testing Instrument ◽  
Infection Surveillance ◽  
Random Intervals ◽  
Screening Platform ◽  
Integrated Screening ◽  
Sentinel Surveillance System

Without any realistic prospect of comprehensive global vaccine coverage and lasting immunity, control of pandemics such as COVID-19 will require implementation of large scale, rapid identification and isolation of infectious individuals to limit further transmission. Here, we describe an automated, high-throughput testing instrument, designed for population-scale testing for SARS-CoV-2 RNA within 25 minutes from inactivated saliva to result, and capable of reporting 3,840 results per hour. This integrated screening platform incorporates continuous flow loading of samples at random intervals to cost-effectively adjust for fluctuations in testing demand. Protecting vulnerable populations during global pandemics requires rapid and sensitive infection surveillance of asymptomatic carriers. This Sentinel surveillance system offers a feasible and scalable approach to complement vaccination, to curb the spread of COVID-19 variants and future pandemics to save lives.

scholarly journals Large-Scale, High-Throughput Validation of Short Hairpin RNA Sequences for RNA Interference

2006 ◽  
Vol 11 (3) ◽  
pp. 236-246 ◽  
Author(s):  
Laurence H. Lamarcq ◽  
Bradley J. Scherer ◽  
Michael L. Phelan ◽  
Nikolai N. Kalnine ◽  
Yen H. Nguyen ◽  
...  
Keyword(s):  
High Throughput ◽  
Large Scale ◽  
Strong Support ◽  
Gc Content ◽  
Rapid Identification ◽  
Hairpin Rna ◽  
Rna Sequences ◽  
Short Hairpin ◽  
Short Hairpin Rnas ◽  
Interfering Rna

A method for high-throughput cloning and analysis of short hairpin RNAs (shRNAs) is described. Using this approach, 464 shRNAs against 116 different genes were screened for knockdown efficacy, enabling rapid identification of effective shRNAs against 74 genes. Statistical analysis of the effects of various criteria on the activity of the shRNAs confirmed that some of the rules thought to govern small interfering RNA (siRNA) activity also apply to shRNAs. These include moderate GC content, absence of internal hairpins, and asymmetric thermal stability. However, the authors did not find strong support for positionspecific rules. In addition, analysis of the data suggests that not all genes are equally susceptible to RNAinterference (RNAi).

scholarly journals Well-Being of Healthcare Workers and the General Public during the COVID-19 Pandemic in Vietnam: An Online Survey

2021 ◽  
Vol 18 (9) ◽  
pp. 4737
Author(s):  
Tuyen Dinh Hoang ◽  
Robert Colebunders ◽  
Joseph Nelson Siewe Fodjo ◽  
Nhan Phuc Thanh Nguyen ◽  
Trung Dinh Tran ◽  
...  
Keyword(s):  
Healthcare Workers ◽  
Large Scale ◽  
Online Survey ◽  
Preventive Measures ◽  
Vaccine Coverage ◽  
Health Sector ◽  
Well Being ◽  
Multivariate Logistic Regression Model ◽  
The Mean ◽  
Restrictive Measures

The COVID-19 pandemic and associated restrictive measures implemented may considerably affect people’s lives. This study aimed to assess the well-being of Vietnamese people after COVID-19 lockdown measures were lifted and life gradually returned to normal. An online survey was organized from 21 to 25 April 2020 among Vietnamese residents aged 18 and over. The survey was launched by the Hue University of Medicine and Pharmacy. The WHO-5 Well-Being Index (scored 0–25) was used to score participants’ well-being. A multivariate logistic regression model was used to determine the predictors of well-being. A total of 1922 responses were analyzed (mean age: 31 years; 30.5% male; 88.2% health professionals or students in the health sector). The mean well-being score was 17.35 ± 4.97. Determinants of a high well-being score (≥13) included older age, eating healthy food, practicing physical exercise, working from home, and adhering to the COVID-19 preventive measures. Female participants, persons worried about their relatives’ health, and smokers were more likely to have a low well-being score. In conclusion, after the lockdown measures were lifted, the Vietnamese have people continued to follow COVID-19 preventive measures, and most of them scored high on the well-being scale. Waiting to achieve large-scale COVID-19 vaccine coverage, promoting preventive COVID-19 measures remains important, together with strategies to guarantee the well-being of the Vietnamese people.

Identifying chironomids (Diptera: Chironomidae) for biological monitoring with PCR–RFLP

2003 ◽  
Vol 93 (6) ◽  
pp. 483-490 ◽  
Author(s):  
M.E. Carew ◽  
V. Pettigrove ◽  
A.A. Hoffmann
Keyword(s):  
Molecular Markers ◽  
Large Scale ◽  
Life Stage ◽  
Biological Indicators ◽  
Geographic Area ◽  
Common Species ◽  
Rapid Identification ◽  
Chironomid Species ◽  
Pcr Rflp ◽  
Identification Of Species

AbstractChironomids are excellent biological indicators for the health of aquatic ecosystems, but their use at finer taxonomic levels is hindered by morphological similarity of species at each life stage. Molecular markers have the potential to overcome these problems by facilitating species identification particularly in large-scale surveys. In this study, the potential of the polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) approach was tested to rapidly distinguish among chironomids within a geographic area, by considering chironomid species from Melbourne, Australia. By comparing molecular markers with diagnostic morphological traits, RFLP profiles of the cytochrome oxidase I (COI) region were identified that were specific to genera and some common species. These profiles were used to develop an RFLP–based key, which was validated by testing the markers on samples from several wetlands and streams. As well as allowing for rapid identification of species that are difficult to separate on morphological grounds, this approach also has the potential to resolve current taxonomic ambiguities.

scholarly journals Progression in Neuroimaging of Normal Pressure Hydrocephalus

2021 ◽  
Vol 12 ◽  
Author(s):  
Rui Yin ◽  
Junxian Wen ◽  
Junji Wei
Keyword(s):  
Future Development ◽  
Normal Pressure Hydrocephalus ◽  
Large Scale ◽  
Elderly Population ◽  
Normal Pressure ◽  
The Elderly ◽  
Rapid Identification ◽  
Clinical Syndrome ◽  
Surgical Interventions ◽  
Large Scale Screening

Normal-pressure hydrocephalus is a clinical syndrome that mainly targets the elderly population. It features dementia, impaired walking, and the malfunction of sphincters. The rapid identification and large-scale screening of patients with normal-pressure hydrocephalus (NPH) are of great significance as surgical interventions can greatly improve or even reverse the symptoms. This review aims to summarize the traditional parameters used to diagnose NPH and the emerging progression in neuroimaging of the disease, hoping to provide an up-to-date overall perspective and summarize the possible direction of its future development.

scholarly journals A Direct-to-Biology High-Throughput Chemistry Approach to Reactive Fragment Screening

2021 ◽  
Author(s):  
Ross P. Thomas ◽  
Rachel E. Heap ◽  
Francesca Zappacosta ◽  
Emma K. Grant ◽  
Peter Pogany ◽  
...  
Keyword(s):  
High Throughput ◽  
Medicinal Chemistry ◽  
Binding Pocket ◽  
Rapid Identification ◽  
Rapid Synthesis ◽  
Iterative Design ◽  
Fragment Screening ◽  
Hit Rate ◽  
Chemical Tools ◽  
Screening Platform

<p>Methods for rapid identification of chemical tools are essential for the validation of emerging targets and to provide medicinal chemistry starting points for the development of <a>new medicines. Here, we report a screening platform that combines ‘direct-to-biology’ high-throughput chemistry (D2B-HTC) with photoreactive covalent fragments. The platform enabled the rapid synthesis of >1000 PhotoAffinity Bits (HTC-PhABits) in 384-well plates. Screening the HTC-PhABit library with </a>carbonic anhydrase I (CAI) afforded 7 hits (0.7% hit rate), which were found to covalently crosslink in the Zn<sup>2+</sup> binding pocket. A powerful advantage of the D2B-HTC screening platform is the ability to rapidly perform iterative design-make-test cycles, accelerating the development and optimisation of chemical tools and medicinal chemistry starting points with little investment of resource.</p>

scholarly journals MetaBMF: a scalable binning algorithm for large-scale reference-free metagenomic studies

2019 ◽  
Vol 36 (2) ◽  
pp. 356-363 ◽  
Author(s):  
Terry Ma ◽  
Di Xiao ◽  
Xin Xing
Keyword(s):  
Large Scale ◽  
Empirical Studies ◽  
Nonnegative Matrix ◽  
Rapid Identification ◽  
Strain Level ◽  
Bacterial Strains ◽  
Binary Matrix ◽  
Next Generation Sequencing Technology ◽  
Microbial Species ◽  
Reference Genomes

Abstract Motivation Metagenomics studies microbial genomes in an ecosystem such as the gastrointestinal tract of a human. Identification of novel microbial species and quantification of their distributional variations among different samples that are sequenced using next-generation-sequencing technology hold the key to the success of most metagenomic studies. To achieve these goals, we propose a simple yet powerful metagenomic binning method, MetaBMF. The method does not require prior knowledge of reference genomes and produces highly accurate results, even at a strain level. Thus, it can be broadly used to identify disease-related microbial organisms that are not well-studied. Results Mathematically, we count the number of mapped reads on each assembled genomic fragment cross different samples as our input matrix and propose a scalable stratified angle regression algorithm to factorize this count matrix into a product of a binary matrix and a nonnegative matrix. The binary matrix can be used to separate microbial species and the nonnegative matrix quantifies the species distributions in different samples. In simulation and empirical studies, we demonstrate that MetaBMF has a high binning accuracy. It can not only bin DNA fragments accurately at a species level but also at a strain level. As shown in our example, we can accurately identify the Shiga-toxigenic Escherichia coli O104: H4 strain which led to the 2011 German E.coli outbreak. Our efforts in these areas should lead to (i) fundamental advances in metagenomic binning, (ii) development and refinement of technology for the rapid identification and quantification of microbial distributions and (iii) finding of potential probiotics or reliable pathogenic bacterial strains. Availability and implementation The software is available at https://github.com/didi10384/MetaBMF.

scholarly journals Technological advancements and their importance for nematode identification

SOIL ◽  
2016 ◽  
Vol 2 (2) ◽  
pp. 257-270 ◽  
Author(s):  
Mohammed Ahmed ◽  
Melanie Sapp ◽  
Thomas Prior ◽  
Gerrit Karssen ◽  
Matthew Alan Back
Keyword(s):  
High Throughput ◽  
Crop Production ◽  
Large Scale ◽  
High Throughput Sequencing ◽  
Biological Indicators ◽  
Rapid Identification ◽  
Community Studies ◽  
Terrestrial Environments ◽  
Traditional Taxonomy ◽  
Sequencing Platforms

Abstract. Nematodes represent a species-rich and morphologically diverse group of metazoans known to inhabit both aquatic and terrestrial environments. Their role as biological indicators and as key players in nutrient cycling has been well documented. Some plant-parasitic species are also known to cause significant losses to crop production. In spite of this, there still exists a huge gap in our knowledge of their diversity due to the enormity of time and expertise often involved in characterising species using phenotypic features. Molecular methodology provides useful means of complementing the limited number of reliable diagnostic characters available for morphology-based identification. We discuss herein some of the limitations of traditional taxonomy and how molecular methodologies, especially the use of high-throughput sequencing, have assisted in carrying out large-scale nematode community studies and characterisation of phytonematodes through rapid identification of multiple taxa. We also provide brief descriptions of some the current and almost-outdated high-throughput sequencing platforms and their applications in both plant nematology and soil ecology.

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