scholarly journals From Alpha to Zeta: Identifying variants and subtypes of SARS-CoV-2 via clustering

2021 ◽  
Author(s):  
Andrew Melnyk ◽  
Fatemeh Mohebbi ◽  
Sergey Knyazev ◽  
Bikram Sahoo ◽  
Roya Hosseini ◽  
...  
Keyword(s):  
Large Datasets ◽  
Genomic Diversity ◽  
Gap Filling ◽  
Novel Variants ◽  
Very Large Datasets ◽  
Clustering Approach ◽  
Alpha Variant ◽  
The Uk ◽  
First Time ◽  
Over Time

The availability of millions of SARS-CoV-2 sequences in public databases such as GISAID and EMBL-EBI (UK) allows a detailed study of the evolution, genomic diversity and dynamics of a virus like never before. Here we identify novel variants and subtypes of SARS-CoV-2 by clustering sequences in adapting methods originally designed for haplotyping intra-host viral populations. We asses our results using clustering entropy --- the first time it has been used in this context. Our clustering approach reaches lower entropies compared to other methods, and we are able to boost this even further through gap filling and Monte Carlo based entropy minimization. Moreover, our method clearly identifies the well-known Alpha variant in the UK and GISAID datasets, but is also able to detect the much less represented (<1% of the sequences) Beta (South Africa), Epsilon (California), Gamma and Zeta (Brazil) variants in the GISAID dataset. Finally, we show that each variant identified has high selective fitness, based on the growth rate of its cluster over time. This demonstrates that our clustering approach is a viable alternative for detecting even rare subtypes in very large datasets.

scholarly journals Screening, Prevention and Treatment of COVID-19 with Special Reference to African-Americans

2021 ◽  
Vol 2 (3) ◽  
pp. 01-06
Author(s):  
Prabir Mandal
Keyword(s):  
South Africa ◽  
Immune Responses ◽  
Severe Illness ◽  
The Novel ◽  
Novel Variants ◽  
Prevention And Treatment ◽  
Previous Infection ◽  
Flu Virus ◽  
The Uk ◽  
Over Time

Viruses mutate all the time, and the coronavirus that causes COVID-19 is no exception. As new variants of the COVID-19 emerge, a slew of new studies suggest that some may be able to evade immune responses triggered by a previous infection or by a vaccine. The novel variants of SARS-CoV-2 including those seen in the UK (2OI/5O1Y.V1/B.1.1.7), South Africa (2OH/5O1Y.V2/B.1.351), Brazil (P.1/2OJ/5O1Y.V3/B.1.1.248) have emerged with the concern of increased infectivity and virulence. Scientists are working to learn more about the characteristics of these strains whether they could cause more severe illness, and whether currently authorized vaccines will protect people against them. All viruses naturally mutate and evolve over time. For example, flu virus change often, which is why doctors recommend that you get a flu shot every year. Various mRNA vaccine platforms have been developed in recent years and validated in studies of immunogenicity and efficacy.

UK Fiscal Squeezes over a Century

2017 ◽  
Author(s):  
Christopher Hood ◽  
Rozana Himaz
Keyword(s):  
Data Sources ◽  
Fiscal Consolidation ◽  
Financial Outcomes ◽  
Financial Conditions ◽  
Deficit Reduction ◽  
Before And After ◽  
The Uk ◽  
Changes Over Time ◽  
Spending Cuts ◽  
Over Time

This chapter draws on historical statistics reporting financial outcomes for spending, taxation, debt, and deficit for the UK over a century to (a) identify quantitatively and compare the main fiscal squeeze episodes (i.e. major revenue increases, spending cuts, or both) in terms of type (soft squeezes and hard squeezes, spending squeezes, and revenue squeezes), depth, and length; (b) compare these periods of austerity against measures of fiscal consolidation in terms of deficit reduction; and (c) identify economic and financial conditions before and after the various squeezes. It explores the extent to which the identification of squeeze episodes and their classification is sensitive to which thresholds are set and what data sources are used. The chapter identifies major changes over time that emerge from this analysis over the changing depth and types of squeeze.

Unsupervised dimensionality reduction for very large datasets: Are we going to the right direction?

2020 ◽  
Vol 196 ◽  
pp. 105777
Author(s):  
Jadson Jose Monteiro Oliveira ◽  
Robson Leonardo Ferreira Cordeiro
Keyword(s):  
Dimensionality Reduction ◽  
Large Datasets ◽  
Very Large Datasets ◽  
The Right

scholarly journals Phylogenomic Evidence of Reinfection and Persistence of SARS-CoV-2: First Report from Colombia

Vaccines ◽  
2021 ◽  
Vol 9 (3) ◽  
pp. 282
Author(s):  
Juan David Ramírez ◽  
Marina Muñoz ◽  
Nathalia Ballesteros ◽  
Luz H. Patiño ◽  
Sergio Castañeda ◽  
...  
Keyword(s):  
Viral Persistence ◽  
Transmission Dynamics ◽  
Polymorphism Analysis ◽  
Rt Pcr ◽  
Paired Samples ◽  
Infection Dynamics ◽  
Oxford Nanopore ◽  
Novel Variants ◽  
First Time ◽  
Oxford Nanopore Technologies

The continuing evolution of SARS-CoV-2 and the emergence of novel variants have raised concerns about possible reinfection events and potential changes in the coronavirus disease 2019 (COVID-19) transmission dynamics. Utilizing Oxford Nanopore technologies, we sequenced paired samples of three patients with positive RT-PCR results in a 1–2-month window period, and subsequent phylogenetics and genetic polymorphism analysis of these genomes was performed. Herein, we report, for the first time, genomic evidence of one case of reinfection in Colombia, exhibiting different SARS-CoV-2 lineage classifications between samples (B.1 and B.1.1.269). Furthermore, we report two cases of possible viral persistence, highlighting the importance of deepening our understanding on the evolutionary intra-host traits of this virus throughout different timeframes of disease progression. These results emphasize the relevance of genomic surveillance as a tool for understanding SARS-CoV-2 infection dynamics, and how this may translate effectively to future control and mitigations efforts, such as the national vaccination program.

scholarly journals Topological and Morphological Controls on Morphodynamics of Salt Marsh Interiors

2021 ◽  
Vol 9 (3) ◽  
pp. 311
Author(s):  
Ben R. Evans ◽  
Iris Möller ◽  
Tom Spencer
Keyword(s):  
Salt Marsh ◽  
Salt Marshes ◽  
East Coast ◽  
Marsh Surface ◽  
Coastal Environments ◽  
Coastal System ◽  
Morphological Segmentation ◽  
The Usa ◽  
The Uk ◽  
Over Time

Salt marshes are important coastal environments and provide multiple benefits to society. They are considered to be declining in extent globally, including on the UK east coast. The dynamics and characteristics of interior parts of salt marsh systems are spatially variable and can fundamentally affect biotic distributions and the way in which the landscape delivers ecosystem services. It is therefore important to understand, and be able to predict, how these landscape configurations may evolve over time and where the greatest dynamism will occur. This study estimates morphodynamic changes in salt marsh areas for a regional domain over a multi-decadal timescale. We demonstrate at a landscape scale that relationships exist between the topology and morphology of a salt marsh and changes in its condition over time. We present an inherently scalable satellite-derived measure of change in marsh platform integrity that allows the monitoring of changes in marsh condition. We then demonstrate that easily derived geospatial and morphometric parameters can be used to determine the probability of marsh degradation. We draw comparisons with previous work conducted on the east coast of the USA, finding differences in marsh responses according to their position within the wider coastal system between the two regions, but relatively consistent in relation to the within-marsh situation. We describe the sub-pixel-scale marsh morphometry using a morphological segmentation algorithm applied to 25 cm-resolution maps of vegetated marsh surface. We also find strong relationships between morphometric indices and change in marsh platform integrity which allow for the inference of past dynamism but also suggest that current morphology may be predictive of future change. We thus provide insight into the factors governing marsh degradation that will assist the anticipation of adverse changes to the attributes and functions of these critical coastal environments and inform ongoing ecogeomorphic modelling developments.

scholarly journals Whole-Genome Sequence Analysis of Pseudorabies Virus Clinical Isolates from Pigs in China between 2012 and 2017 in China

Viruses ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1322
Author(s):  
Ruiming Hu ◽  
Leyi Wang ◽  
Qingyun Liu ◽  
Lin Hua ◽  
Xi Huang ◽  
...  
Keyword(s):  
Selection Pressure ◽  
Pseudorabies Virus ◽  
Viral Evolution ◽  
Infectious Agent ◽  
Genomic Diversity ◽  
Whole Genome Sequence ◽  
Evolutionary Constraint ◽  
The Novel ◽  
Novel Variants ◽  
Pressure Analysis

Pseudorabies virus (PRV) is an economically significant swine infectious agent. A PRV outbreak took place in China in 2011 with novel virulent variants. Although the association of viral genomic variability with pathogenicity is not fully confirmed, the knowledge concerning PRV genomic diversity and evolution is still limited. Here, we sequenced 54 genomes of novel PRV variants isolated in China from 2012 to 2017. Phylogenetic analysis revealed that China strains and US/Europe strains were classified into two separate genotypes. PRV strains isolated from 2012 to 2017 in China are highly related to each other and genetically close to classic China strains such as Ea, Fa, and SC. RDP analysis revealed 23 recombination events within novel PRV variants, indicating that recombination contributes significantly to the viral evolution. The selection pressure analysis indicated that most ORFs were under evolutionary constraint, and 19 amino acid residue sites in 15 ORFs were identified under positive selection. Additionally, 37 unique mutations were identified in 19 ORFs, which distinguish the novel variants from classic strains. Overall, our study suggested that novel PRV variants might evolve from classical PRV strains through point mutation and recombination mechanisms.

scholarly journals Resource and waste quantification scenarios for wind turbine decommissioning in the United Kingdom

2020 ◽  
Author(s):  
Kiran Tota-Maharaj ◽  
Alexander McMahon
Keyword(s):  
United Kingdom ◽  
Waste Management ◽  
Wind Turbine ◽  
End Of Life ◽  
Wind Turbines ◽  
Rapid Rise ◽  
The United Kingdom ◽  
Management Procedures ◽  
The Uk ◽  
Over Time

AbstractWind power produces more electricity than any other form of renewable energy in the United Kingdom (UK) and plays a key role in decarbonisation of the grid. Although wind energy is seen as a sustainable alternative to fossil fuels, there are still several environmental impacts associated with all stages of the lifecycle of a wind farm. This study determined the material composition for wind turbines for various sizes and designs and the prevalence of such turbines over time, to accurately quantify waste generation following wind turbine decommissioning in the UK. The end of life stage is becoming increasingly important as a rapid rise in installation rates suggests an equally rapid rise in decommissioning rates can be expected as wind turbines reach the end of their 20–25-year operational lifetime. Waste data analytics were applied in this study for the UK in 5-year intervals, stemming from 2000 to 2039. Current practices for end of life waste management procedures have been analysed to create baseline scenarios. These scenarios have been used to explore potential waste management mitigation options for various materials and components such as reuse, remanufacture, recycling, and heat recovery from incineration. Six scenarios were then developed based on these waste management options, which have demonstrated the significant environmental benefits of such practices through quantification of waste reduction and greenhouse gas (GHG) emissions savings. For the 2015–2019 time period, over 35 kilotonnes of waste are expected to be generated annually. Overall waste is expected to increase over time to more than 1200 kilotonnes annually by 2039. Concrete is expected to account for the majority of waste associated with wind turbine decommissioning initially due to foundations for onshore turbines accounting for approximately 80% of their total weight. By 2035–2039, steel waste is expected to account for almost 50% of overall waste due to the emergence of offshore turbines, the foundations of which are predominantly made of steel.

scholarly journals In-work Universal Credit: Claimant Experiences of Conditionality Mismatches and Counterproductive Benefit Sanctions

2020 ◽  
pp. 1-19
Author(s):  
SHARON WRIGHT ◽  
PETER DWYER
Keyword(s):  
Social Security ◽  
Job Search ◽  
Longitudinal Research ◽  
Working Hours ◽  
Unique Contribution ◽  
Working Age ◽  
Micro Level ◽  
Benefit Sanctions ◽  
The Uk ◽  
Over Time

Abstract Universal Credit is the UK’s globally innovative social security reform that replaces six means tested benefits with one monthly payment for working age claimants - combining social security and tax credit systems. Universal Credit expands welfare conditionality via mandatory job search conditions to enhance ‘progression’ amongst working claimants by requiring extra working hours or multiple jobs. This exposes low paid workers to tough benefit sanctions for non-compliance, which could remove essential income indefinitely or for fixed periods of up to three years. Our unique contribution is to establish how this new regime is experienced at micro level by in-work claimants over time. We present findings from Qualitative Longitudinal Research (141 interviews with 58 claimants, 2014-17), to demonstrate how UC impacts on in-work recipients and how conditionality produces a new coerced worker-claimant model of social support. We identify a series of welfare conditionality mismatches and conclude that conditionality for in-work claimants is largely counterproductive. This implies a redesign of the UK system and serves as an international warning to potential policy emulators.

scholarly journals Prolonged efficacy of pembrolizumab in a patient presenting a multi-treated metastatic hepatocholangiocarcinoma

2020 ◽  
Vol 13 ◽  
pp. 175628482093518 ◽  
Author(s):  
Angélique Saint ◽  
Maxime Benchetrit ◽  
Sébastien Novellas ◽  
Denis Ouzan ◽  
Alexander Tuan Falk ◽  
...  
Keyword(s):  
Therapeutic Strategy ◽  
Complete Response ◽  
It Management ◽  
Tumor Control ◽  
Line Treatment ◽  
Viral Hepatitis C ◽  
Programmed Cell Death 1 ◽  
First Time ◽  
Inhibitor Treatment ◽  
Over Time

Introduction: Hepatocholangiocarcinoma (HCC-ICC) is a rare tumor presenting the histologic characteristics of both hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (ICC). As there is no consensus on it management, the therapeutic strategy rests on the specific treatments for HCC or ICC. Programmed cell death 1 (PD-1) inhibitors showed encouraging results in the second line treatment of HCC after sorafenib but it efficacy in HCC-ICC has never been reported. Methods and results: We present the case of a 72-year-old male patient treated for metastatic HCC-ICC due to a viral hepatitis C cirrhosis in progression after two lines of treatment. Tumor was characterized by a PDL-1 status of 85%. Patient received pembrolizumab at doses of 200 mg every 21 days by intravenous infusion. After one injection he was presented an immediate clinical benefit, a partial response was observed after two months of treatment and a complete response two months later. This response was maintained over time along with toxicity-free tumor control after 18 months treatment. Conclusion: To our knowledge, we reported for the first time the efficacy of a PD1 inhibitor treatment in a patient presenting metastatic HCC-ICC due to viral cirrhosis and overexpressing PDL-1 after failure of two lines of treatment.

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