Optimizing Combination of Parameters for Pull-off Adhesion Testing through Design of Experiment Study

A minimum of adhesion strength of thin films and coatings to substrates is required for their durable applications. Practical Adhesion is measure of that strength required to pull-off coating or film from the substrate. A suitable method to measure this adhesion strength has to be one that allows quantitative repeatable hence reliable results. There are many methods and techniques to measure this practical adhesion. However, none inclusively quantifies adhesion with repeatable results. Pull-Off method involves application of tensile forces and delivers quantitative results. Here we report optimizations made in combination of parameters for Pull-Off adhesion testing. Optimized combination of adhesive mixing ratio, time for hardening (curing), time to test after hardening and applied force rate was achieved through detailed Design of Experiment study. Achieved combination delivered results which were quantitative, repeatable, consistent and uniform and allowed application of method to a variety of coatings and films with enhanced reliability. The improvements here in reported are applicable to majority of thin films and coating systems delivering some standardized parameters combination for pull-off method

Stability of SARS-CoV-2 phylogenies.

Funder: Alfred P. Sloan Foundation; funder-id: http://dx.doi.org/10.13039/100000879Funder: European Molecular Biology Laboratory (EMBL)The SARS-CoV-2 pandemic has led to unprecedented, nearly real-time genetic tracing due to the rapid community sequencing response. Researchers immediately leveraged these data to infer the evolutionary relationships among viral samples and to study key biological questions, including whether host viral genome editing and recombination are features of SARS-CoV-2 evolution. This global sequencing effort is inherently decentralized and must rely on data collected by many labs using a wide variety of molecular and bioinformatic techniques. There is thus a strong possibility that systematic errors associated with lab-or protocol-specific practices affect some sequences in the repositories. We find that some recurrent mutations in reported SARS-CoV-2 genome sequences have been observed predominantly or exclusively by single labs, co-localize with commonly used primer binding sites and are more likely to affect the protein-coding sequences than other similarly recurrent mutations. We show that their inclusion can affect phylogenetic inference on scales relevant to local lineage tracing, and make it appear as though there has been an excess of recurrent mutation or recombination among viral lineages. We suggest how samples can be screened and problematic variants removed, and we plan to regularly inform the scientific community with our updated results as more SARS-CoV-2 genome sequences are shared (https://virological.org/t/issues-with-sars-cov-2-sequencing-data/473 and https://virological.org/t/masking-strategies-for-sars-cov-2-alignments/480). We also develop tools for comparing and visualizing differences among very large phylogenies and we show that consistent clade- and tree-based comparisons can be made between phylogenies produced by different groups. These will facilitate evolutionary inferences and comparisons among phylogenies produced for a wide array of purposes. Building on the SARS-CoV-2 Genome Browser at UCSC, we present a toolkit to compare, analyze and combine SARS-CoV-2 phylogenies, find and remove potential sequencing errors and establish a widely shared, stable clade structure for a more accurate scientific inference and discourse

phastSim: Efficient simulation of sequence evolution for pandemic-scale datasets.

Sequence simulators are fundamental tools in bioinformatics, as they allow us to test data processing and inference tools, and are an essential component of some inference methods. The ongoing surge in available sequence data is however testing the limits of our bioinformatics software. One example is the large number of SARS-CoV-2 genomes available, which are beyond the processing power of many methods, and simulating such large datasets is also proving difficult. Here, we present a new algorithm and software for efficiently simulating sequence evolution along extremely large trees (e.g. > 100, 000 tips) when the branches of the tree are short, as is typical in genomic epidemiology. Our algorithm is based on the Gillespie approach, and it implements an efficient multi-layered search tree structure that provides high computational efficiency by taking advantage of the fact that only a small proportion of the genome is likely to mutate at each branch of the considered phylogeny. Our open source software allows easy integration with other Python packages as well as a variety of evolutionary models, including indel models and new hypermutability models that we developed to more realistically represent SARS-CoV-2 genome evolution

phastSim: Efficient simulation of sequence evolution for pandemic-scale datasets.

Funder: European Molecular Biology LaboratoryFunder: Schmidt Futures FoundationSequence simulators are fundamental tools in bioinformatics, as they allow us to test data processing and inference tools, and are an essential component of some inference methods. The ongoing surge in available sequence data is however testing the limits of our bioinformatics software. One example is the large number of SARS-CoV-2 genomes available, which are beyond the processing power of many methods, and simulating such large datasets is also proving difficult. Here, we present a new algorithm and software for efficiently simulating sequence evolution along extremely large trees (e.g. > 100, 000 tips) when the branches of the tree are short, as is typical in genomic epidemiology. Our algorithm is based on the Gillespie approach, and it implements an efficient multi-layered search tree structure that provides high computational efficiency by taking advantage of the fact that only a small proportion of the genome is likely to mutate at each branch of the considered phylogeny. Our open source software allows easy integration with other Python packages as well as a variety of evolutionary models, including indel models and new hypermutability models that we developed to more realistically represent SARS-CoV-2 genome evolution

Stability of SARS-CoV-2 phylogenies.

The SARS-CoV-2 pandemic has led to unprecedented, nearly real-time genetic tracing due to the rapid community sequencing response. Researchers immediately leveraged these data to infer the evolutionary relationships among viral samples and to study key biological questions, including whether host viral genome editing and recombination are features of SARS-CoV-2 evolution. This global sequencing effort is inherently decentralized and must rely on data collected by many labs using a wide variety of molecular and bioinformatic techniques. There is thus a strong possibility that systematic errors associated with lab-or protocol-specific practices affect some sequences in the repositories. We find that some recurrent mutations in reported SARS-CoV-2 genome sequences have been observed predominantly or exclusively by single labs, co-localize with commonly used primer binding sites and are more likely to affect the protein-coding sequences than other similarly recurrent mutations. We show that their inclusion can affect phylogenetic inference on scales relevant to local lineage tracing, and make it appear as though there has been an excess of recurrent mutation or recombination among viral lineages. We suggest how samples can be screened and problematic variants removed, and we plan to regularly inform the scientific community with our updated results as more SARS-CoV-2 genome sequences are shared (https://virological.org/t/issues-with-sars-cov-2-sequencing-data/473 and https://virological.org/t/masking-strategies-for-sars-cov-2-alignments/480). We also develop tools for comparing and visualizing differences among very large phylogenies and we show that consistent clade- and tree-based comparisons can be made between phylogenies produced by different groups. These will facilitate evolutionary inferences and comparisons among phylogenies produced for a wide array of purposes. Building on the SARS-CoV-2 Genome Browser at UCSC, we present a toolkit to compare, analyze and combine SARS-CoV-2 phylogenies, find and remove potential sequencing errors and establish a widely shared, stable clade structure for a more accurate scientific inference and discourse

High-speed volumetric imaging of neuronal activity in freely moving rodents

Thus far, optical recording of neuronal activity in freely behaving animals has been limited to a thin axial range. We present a head-mounted miniaturized light-field microscope (MiniLFM) capable of capturing neuronal network activity within a volume of 700 × 600 × 360 µm3 at 16 Hz in the hippocampus of freely moving mice. We demonstrate that neurons separated by as little as ~15 µm and at depths up to 360 µm can be discriminated

Ocorrência de vírus em batata em sete estados do Brasil Virus occurrence in potatoes in seven Brazilian States

As viroses causam rápida degenerescência dos tubérculos-sementes de batata. Em condições tropicais, em que a presença de afídeos vetores é constante e a estrutura das populações de vírus é dinâmica, a pressão das doenças é enorme. Conhecer essa dinâmica é uma ferramenta importante para a sustentabilidade da produção de batata. Realizou-se um levantamento abrangente da ocorrência de viroses em batata no Brasil, além de estudar-se a distribuição das estirpes de Potato virus Y (PVY) associadas ao mosaico da batata. Em 2005 e 2006 foram visitadas lavouras em sete estados brasileiros, coletando-se folíolos com sintomas de viroses (1.256 amostras) e amostras aleatórias (360 amostras). Foi feita também uma estimativa visual da incidência de mosaico e enrolamento-das-folhas em vários dos campos visitados. Das 1.256 amostras suspeitas, 840 apresentaram reação positiva em teste sorológico para PVY (66,9%), 128 para Potato leaf roll virus (PLRV) (10,2%), 79 para Potato virus S (PVS) (6,3%) e nenhuma para Potato virus X (PVX). Os resultados dos testes de detecção por DAS-ELISA, biológico e RT-PCR mostraram a presença quase absoluta do subgrupo necrótico de PVY, em sua maioria PVY NTN. A análise de uma sub-amostragem em todos os municípios visitados confirmou que essa variante está hoje presente nos sete estados visitados. Amostras de PVY NTN foram obtidas das cultivares Asterix, Atlantic, Agata, Achat, Baronesa, Baraka, Bintje, Caesar, Cupido, Marijke, Monalisa, Panda e Vivaldi, que apresentaram diferentes níveis de suscetibilidade. As amostras aleatórias revelaram um quadro muito similar ao encontrado com as amostras sintomáticas. PLRV foi identificado em MG, BA, PR e SC, em várias lavouras de forma muito freqüente. PVS foi identificado nesses mesmos estados e também em SP. PVX foi detectado em apenas uma amostra tomada ao acaso em Serra do Salitre (MG). O contraste entre a avaliação visual dos sintomas e os resultados do teste de detecção por ELISA revelou a possibilidade de infecção latente por PVY em níveis relevantes na cultivar Asterix.<br>Viruses are responsible for the quick degeneration of potato seed-tubers. In the tropics, where aphid vectors are constantly present and the structure of virus populations is dynamic, the disease pressure is enormous. Therefore, the knowledge of such dynamics is definitely an extremely valuable tool towards the sustainability of the national potato production. In this study, we report a broad survey of virus occurrence in potato, in Brazil. In addition, we studied the distribution of the Potato virus Y (PVY) strains associated with mosaic symptoms on potatoes. In 2005 and 2006, we visited potato fields in seven Brazilian States. We collected leaves of symptomatic plants (1,256 samples) and also at random (360 samples). In addition, in several fields a visual assessment was carried out to estimate mosaic and leafroll incidence. From the 1,256 samples with symptoms, 840 tested serologically were positive to PVY (66.9%), 128 to PLRV (10.2%), 79 to PVS (6.3%), and none to PVX. Serology using DAS-ELISA and also biological and RT-PCR tests revealed an almost exclusive occurrence of the PVY necrotic strain, predominantly the necrotic subgroup PVY NTN. The analysis of a sub-sample representing all surveyed Counties indicated that the necrotic strain was universally present. Cultivars Asterix, Atlantic, Agata, Achat, Baronesa, Baraka, Bintje, Caesar, Cupido, Marijke, Monalisa, Panda, and Vivaldi, although displaying different susceptibility levels, were all infected by PVY NTN. The analysis of leaves collected at random showed similar results. PLRV was identified in four States (Minas Gerais, Bahia, Paraná, and Santa Catarina), while PVS was present in the State of São Paulo as well. PVX was found in only one sample collected at random in Serra do Salitre, State of Minas Gerais. The contrast between visual evaluation and the results of the detection test by ELISA strongly indicated the presence of a relevant rate of PVY latent infection on cultivar Asterix