scholarly journals Direct sequencing of measles virus complete genomes in the midst of a large-scale outbreak

PLoS ONE ◽  
2021 ◽  
Vol 16 (9) ◽  
pp. e0255663
Author(s):  
Efrat Bucris ◽  
Victoria Indenbaum ◽  
Roberto Azar ◽  
Oran Erster ◽  
Eric Haas ◽  
...  
Keyword(s):  
High Resolution ◽  
In Silico ◽  
Measles Virus ◽  
Large Scale ◽  
Direct Sequencing ◽  
Limited Resource ◽  
Average Depth ◽  
Genome Coverage ◽  
Complete Genomes ◽  
Measles Outbreaks

Measles outbreaks escalated globally despite worldwide elimination efforts. Molecular epidemiological investigations utilizing partial measles virus (MeV) genomes are challenged by reduction in global genotypes and low evolutionary rates. Greater resolution was reached using MeV complete genomes, however time and costs limit the application to numerous samples. We developed an approach to unbiasedly sequence complete MeV genomes directly from patient urine samples. Samples were enriched for MeV using filtration or nucleases and the minimal number of sequence reads to allocate per sample based on its MeV content was assessed using in-silico reduction of sequencing depth. Application of limited-resource sequencing to treated MeV-positive samples demonstrated that 1–5 million sequences for samples with high/medium MeV quantities and 10–15 million sequences for samples with lower MeV quantities are sufficient to obtain >98% MeV genome coverage and over X50 average depth. This approach enables real-time high-resolution molecular epidemiological investigations of large-scale MeV outbreaks.

MEASLES VIRUS ELIMINATION: RESOLVED ISSUES AND FUTURE CHALLENGES

2020 ◽  
pp. 83-88
Author(s):  
Kseniia Artemivna Veklych
Keyword(s):  
Measles Virus ◽  
Disease Outbreaks ◽  
Vaccination Schedule ◽  
Successful Implementation ◽  
Complete Elimination ◽  
Virus Elimination ◽  
Vaccination Programs ◽  
Future Challenges ◽  
The Moment ◽  
Measles Outbreaks

Measles is a highly contagious infectious disease caused by an RNA−containing virus of the family Paramyxoviridae and Morbillivirus genus. The most proper way to stop it is a total vaccination. At the moment, live attenuated strains of the Enders − Schwartz measles virus are used to conduct it. Although they were developed more than 50 years ago, the vaccines in use today are effective enough to create a proper immune protection that can defend against an infection for decades, if the vaccination schedule is followed. The vast majority of measles outbreaks that have been reported in Europe over the last seven years have been caused by a lack of an immune response resulting from the unprecedented coverage of the population with vaccination. The measles outbreak observed in the adult and child population of Ukraine since December 2018 indicates the need and urgency of additional efforts to curb the spread and complete elimination of the measles virus. It has been determined that more than 95 % of the population should be vaccinated to ensure an elimination of measles virus and prevent the disease outbreaks after the virus has been imported from the countries that are still endemic to measles. It is noted that as a result of successful implementation of vaccination programs, the public's attention to measles is diminished even among physicians who sometimes have a rather dubious understanding of the disease symptoms. Ensuring a complete elimination of the measles virus requires the development and implementation of additional laboratory tests for immunity, development and realization of new, more polyvalent vaccines that are more readily accepted by population, increased awareness on safety and necessity of vaccination, as well as regulation. Key words: measles, immunity, elimination, epidemiological control, vaccination.

MODELING THE SOUTH ATLANTIC OCEAN FROM MEDIUM TO HIGH RESOLUTION

2014 ◽  
Vol 31 (2) ◽  
Author(s):  
Mariela Gabioux ◽  
Vladimir Santos da Costa ◽  
Joao Marcos Azevedo Correia de Souza ◽  
Bruna Faria de Oliveira ◽  
Afonso De Moraes Paiva
Keyword(s):  
High Resolution ◽  
Atlantic Ocean ◽  
Large Scale ◽  
South Atlantic ◽  
Surface Relaxation ◽  
The South ◽  
Small Surface ◽  
Basic Model ◽  
Basic Set ◽  
Set Up

Results of the basic model configuration of the REMO project, a Brazilian approach towards operational oceanography, are discussed. This configuration consists basically of a high-resolution eddy-resolving, 1/12 degree model for the Metarea V, nested in a medium-resolution eddy-permitting, 1/4 degree model of the Atlantic Ocean. These simulations performed with HYCOM model, aim for: a) creating a basic set-up for implementation of assimilation techniques leading to ocean prediction; b) the development of hydrodynamics bases for environmental studies; c) providing boundary conditions for regional domains with increased resolution. The 1/4 degree simulation was able to simulate realistic equatorial and south Atlantic large scale circulation, both the wind-driven and the thermohaline components. The high resolution simulation was able to generate mesoscale and represent well the variability pattern within the Metarea V domain. The BC mean transport values were well represented in the southwestern region (between Vitória-Trinidade sea mount and 29S), in contrast to higher latitudes (higher than 30S) where it was slightly underestimated. Important issues for the simulation of the South Atlantic with high resolution are discussed, like the ideal place for boundaries, improvements in the bathymetric representation and the control of bias SST, by the introducing of a small surface relaxation. In order to make a preliminary assessment of the model behavior when submitted to data assimilation, the Cooper & Haines (1996) method was used to extrapolate SSH anomalies fields to deeper layers every 7 days, with encouraging results.

scholarly journals Author Correction: High-resolution, large-scale laboratory measurements of a sandy beach and dynamic cobble berm revetment

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Chris E. Blenkinsopp ◽  
Paul M. Bayle ◽  
Daniel C. Conley ◽  
Gerd Masselink ◽  
Emily Gulson ◽  
...  
Keyword(s):  
High Resolution ◽  
Large Scale ◽  
Sandy Beach ◽  
Laboratory Measurements

A Correction to this paper has been published: https://doi.org/10.1038/s41597-021-00874-2.

scholarly journals Rapid Single Image-Based DTM Estimation from ExoMars TGO CaSSIS Images Using Generative Adversarial U-Nets

2021 ◽  
Vol 13 (15) ◽  
pp. 2877
Author(s):  
Yu Tao ◽  
Siting Xiong ◽  
Susan J. Conway ◽  
Jan-Peter Muller ◽  
Anthony Guimpier ◽  
...  
Keyword(s):  
High Resolution ◽  
Large Scale ◽  
Imaging System ◽  
Landing Site ◽  
Parameter Tuning ◽  
Processing Parameters ◽  
Input Image ◽  
Large Area ◽  
Laser Altimeter ◽  
Imaging Science

The lack of adequate stereo coverage and where available, lengthy processing time, various artefacts, and unsatisfactory quality and complexity of automating the selection of the best set of processing parameters, have long been big barriers for large-area planetary 3D mapping. In this paper, we propose a deep learning-based solution, called MADNet (Multi-scale generative Adversarial u-net with Dense convolutional and up-projection blocks), that avoids or resolves all of the above issues. We demonstrate the wide applicability of this technique with the ExoMars Trace Gas Orbiter Colour and Stereo Surface Imaging System (CaSSIS) 4.6 m/pixel images on Mars. Only a single input image and a coarse global 3D reference are required, without knowing any camera models or imaging parameters, to produce high-quality and high-resolution full-strip Digital Terrain Models (DTMs) in a few seconds. In this paper, we discuss technical details of the MADNet system and provide detailed comparisons and assessments of the results. The resultant MADNet 8 m/pixel CaSSIS DTMs are qualitatively very similar to the 1 m/pixel HiRISE DTMs. The resultant MADNet CaSSIS DTMs display excellent agreement with nested Mars Reconnaissance Orbiter Context Camera (CTX), Mars Express’s High-Resolution Stereo Camera (HRSC), and Mars Orbiter Laser Altimeter (MOLA) DTMs at large-scale, and meanwhile, show fairly good correlation with the High-Resolution Imaging Science Experiment (HiRISE) DTMs for fine-scale details. In addition, we show how MADNet outperforms traditional photogrammetric methods, both on speed and quality, for other datasets like HRSC, CTX, and HiRISE, without any parameter tuning or re-training of the model. We demonstrate the results for Oxia Planum (the landing site of the European Space Agency’s Rosalind Franklin ExoMars rover 2023) and a couple of sites of high scientific interest.

scholarly journals Parental mosaicism in Marfan and Ehlers–Danlos syndromes and related disorders

2021 ◽  
Author(s):  
Bertrand Chesneau ◽  
Aurélie Plancke ◽  
Guillaume Rolland ◽  
Nicolas Chassaing ◽  
Christine Coubes ◽  
...  
Keyword(s):  
High Resolution ◽  
Marfan Syndrome ◽  
High Resolution Melting ◽  
De Novo ◽  
Direct Sequencing ◽  
Causal Variant ◽  
Connective Tissue Disorder ◽  
High Resolution Melting Analysis ◽  
Aortic Diseases ◽  
Melting Analysis

AbstractMarfan syndrome (MFS) is a heritable connective tissue disorder (HCTD) caused by pathogenic variants in FBN1 that frequently occur de novo. Although individuals with somatogonadal mosaicisms have been reported with respect to MFS and other HCTD, the overall frequency of parental mosaicism in this pathology is unknown. In an attempt to estimate this frequency, we reviewed all the 333 patients with a disease-causing variant in FBN1. We then used direct sequencing, combined with High Resolution Melting Analysis, to detect mosaicism in their parents, complemented by NGS when a mosaicism was objectivized. We found that (1) the number of apparently de novo events is much higher than the classically admitted number (around 50% of patients and not 25% as expected for FBN1) and (2) around 5% of the FBN1 disease-causing variants were not actually de novo as anticipated, but inherited in a context of somatogonadal mosaicisms revealed in parents from three families. High Resolution Melting Analysis and NGS were more efficient at detecting and evaluating the level of mosaicism compared to direct Sanger sequencing. We also investigated individuals with a causal variant in another gene identified through our “aortic diseases genes” NGS panel and report, for the first time, on an individual with a somatogonadal mosaicism in COL5A1. Our study shows that parental mosaicism is not that rare in Marfan syndrome and should be investigated with appropriate methods given its implications in patient’s management.

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