scholarly journals CoVizu: Rapid analysis and visualization of the global diversity of SARS-CoV-2 genomes

2021 ◽  
Author(s):  
Roux-Cil Ferreira ◽  
Emmanuel Wong ◽  
Gopi Gugan ◽  
Kaitlyn Wade ◽  
Molly Liu ◽  
...  
Keyword(s):  
Horizontal Line ◽  
Consensus Tree ◽  
New Approach ◽  
Genomic Epidemiology ◽  
Large Numbers ◽  
Rapid Accumulation ◽  
Global Spread ◽  
Incomplete Coverage ◽  
Collection Date ◽  
Strict Molecular Clock

Phylogenetics has played a pivotal role in the genomic epidemiology of SARS-CoV-2, such as tracking the emergence and global spread of variants, and scientific communication. However, the rapid accumulation of genomic data from around the world - with over two million genomes currently available in the GISAID database - is testing the limits of standard phylogenetic methods. Here, we describe a new approach to rapidly analyze and visualize large numbers of SARS-CoV-2 genomes. Using Python, genomes are filtered for problematic sites, incomplete coverage, and excessive divergence from a strict molecular clock. All differences from the reference genome, including indels, are extracted using minimap2, and compactly stored as a set of features for each genome. For each Pango lineage (https://cov-lineages.org), we collapse genomes with identical features into 'variants', generate 100 bootstrap samples of the feature set union to generate weights, and compute the symmetric differences between the weighted feature sets for every pair of variants. The resulting distance matrices are used to generate neigihbor-joining trees in RapidNJ and converted into a majority-rule consensus tree for the lineage. Branches with support values below 50% or mean lengths below 0.5 differences are collapsed, and tip labels on affected branches are mapped to internal nodes as directly-sampled ancestral variants. Currently, we process about 1.6 million genomes in approximately nine hours on 34 cores. The resulting trees are visualized using the JavaScript framework D3.js as 'beadplots', in which variants are represented by horizontal line segments, annotated with beads representing samples by collection date. Variants are linked by vertical edges to represent branches in the consensus tree. These visualizations are published at https://filogeneti.ca/CoVizu. All source code was released under an MIT license at https://github.com/PoonLab/covizu.

scholarly journals Genomic epidemiology of Vibrio cholerae reveals the regional and global spread of two epidemic non-toxigenic lineages

2020 ◽  
Vol 14 (2) ◽  
pp. e0008046 ◽  
Author(s):  
Haoqiu Wang ◽  
Chao Yang ◽  
Zhou Sun ◽  
Wei Zheng ◽  
Wei Zhang ◽  
...  
Keyword(s):  
Vibrio Cholerae ◽  
Genomic Epidemiology ◽  
Global Spread

scholarly journals Ward floors and other surfaces as reservoirs of hospital infection

1967 ◽  
Vol 65 (4) ◽  
pp. 515-536 ◽  
Author(s):  
G. A. J. Ayliffe ◽  
B. J. Collins ◽  
E. J. L. Lowbury ◽  
J. R. Babb ◽  
H. A. Lilly
Keyword(s):  
Bacterial Contamination ◽  
Hospital Infection ◽  
Staph Aureus ◽  
Air Movement ◽  
Large Numbers ◽  
Equilibrium Level ◽  
Rapid Accumulation ◽  
Floor Surfaces ◽  
Contaminated Area

Impression plates from initially clean horizontal surfaces and floor areas in surgical wards showed a rapid accumulation of bacteria, mainly micrococci, which reached a fluctuating equilibrium after about 24 h. A later increase in bacterial contamination (mainly with aerobic sporing bacilli) to a higher equilibrium level after about 14 days occurred on uncleaned areas. Walls, even if left unwashed, acquired very few bacteria, but many were deposited locally when the wall was touched by a subject whose skin carried large numbers of staphylococci; moist exposed plaster was also heavily contaminated.Regular use of a disinfectant (‘Sudol’ 1 in 100) in cleaning a ward floor did not reduce the equilibrium level of bacteria on the floor.The transfer of staphylococci from contaminated to clean areas on the soles of shoes was demonstrated; the use of tacky and disinfectant mats did not appreciably reduce the transfer of bacteria by this route.Staphylococci deposited on a wall by a disperser were shown to be transferred from the contaminated area of wall to the hands of another subject who did not previously carry the organism; this subject was shown to transfer the staphylo-coccus to a wall which he touched.Attempts to redisperse by air movementStaph. aureuswhich had been shed by a disperser or by a contaminated blanket on to the floor surfaces had little effect; neither blowing with a hair dryer nor brisk exercise appeared to lift any of the staphylococci from a vinyl surface, and only small numbers were lifted by these measures from a terrazzo surface.The hazards of infection from the inanimate environment are discussed.

scholarly journals Structure-mining: screening structure models by automated fitting to the atomic pair distribution function over large numbers of models

2020 ◽  
Vol 76 (3) ◽  
pp. 395-409 ◽  
Author(s):  
Long Yang ◽  
Pavol Juhás ◽  
Maxwell W. Terban ◽  
Matthew G. Tucker ◽  
Simon J. L. Billinge
Keyword(s):  
Distribution Function ◽  
Pair Distribution Function ◽  
Complex Oxide ◽  
Web Based ◽  
New Approach ◽  
Atomic Pair Distribution Function ◽  
Large Numbers ◽  
Traditional Structure ◽  
Atomic Pair ◽  
Atomic Crystal

A new approach is presented to obtain candidate structures from atomic pair distribution function (PDF) data in a highly automated way. It fetches, from web-based structural databases, all the structures meeting the experimenter's search criteria and performs structure refinements on them without human intervention. It supports both X-ray and neutron PDFs. Tests on various material systems show the effectiveness and robustness of the algorithm in finding the correct atomic crystal structure. It works on crystalline and nanocrystalline materials including complex oxide nanoparticles and nanowires, low-symmetry and locally distorted structures, and complicated doped and magnetic materials. This approach could greatly reduce the traditional structure searching work and enable the possibility of high-throughput real-time auto-analysis PDF experiments in the future.

scholarly journals Museum Moving to Inpatients: Le Louvre à l’Hôpital

2019 ◽  
Vol 16 (2) ◽  
pp. 206 ◽  
Author(s):  
Jean-Jacques Monsuez ◽  
Véronique François ◽  
Robert Ratiney ◽  
Isabelle Trinchet ◽  
Pierre Polomeni ◽  
...  
Keyword(s):  
Quality Of Life ◽  
Depressive Symptoms ◽  
New Approach ◽  
Individual Preferences ◽  
Art Program ◽  
Large Numbers ◽  
Art Activities ◽  
One Year ◽  
Large Painting

Anxiety and depressive symptoms are common in hospitalized patients. Arts and cultural programs were reported to enhance their quality of life. The Le Louvre à l’hôpital study presents a new approach in which the museum moves to the hospital by displaying and discussing artworks with patients interactively. Over one year, four large statues were disposed in the hospital gardens, 30 reprints of large painting were exhibited in the hospital hall, dining rooms, and circulations areas. A total of 83 small-group guided art discussions (90 min) were organized, which 451 patients attended. The 200 small-size reproductions of paintings placed in the patients’ rooms were chosen based on their individual preferences. Decreased anxiety after the art sessions was reported by 160 of 201 patients (79.6%). Out of 451 patients, 406 (90%) said the art program had met their expectations, and 372 (82.4%) wished to continue the experience with caregivers (162 paramedics trained for art activity during 66 workshops). In conclusion, moving the museum to the hospital constitutes a valuable way to provide art activities for inpatients in large numbers, which may reduce hospital-related anxiety in many instances.

The evolutionary bootstrap: a new approach to the study of taxonomic diversity

Paleobiology ◽  
1986 ◽  
Vol 12 (3) ◽  
pp. 251-268 ◽  
Author(s):  
Norman L. Gilinsky ◽  
Richard K. Bambach
Keyword(s):  
Null Hypothesis ◽  
Dynamic Properties ◽  
Taxonomic Diversity ◽  
New Approach ◽  
The Real ◽  
Statistical Verification ◽  
Large Numbers ◽  
Random Expectation ◽  
History Of ◽  
End Members

The evolutionary bootstrap is a new approach to the analysis of patterns of taxonomic diversity. In general, the evolutionary bootstrap works by surveying the diversity history of a taxon, learning its dynamic properties, and then generating randomly large numbers of artificial diversity histories based upon what was learned. The distribution of artificial—or bootstrapped—diversity histories approximates the distribution of diversity histories that were possible for taxa with the dynamic properties of the real taxon, and serves as a paleontological null hypothesis for studying statistically the diversity history of the real taxon.Two null hypotheses were established, the additive and the multiplicative. The additive null hypothesis assumes that the amount of diversity change that occurs in a higher taxon during an interval of time is independent of the number of member subtaxa present at the beginning of the interval. The multiplicative null hypothesis, in contrast, assumes that the amount of diversity change that occurs is dependent upon the number of member subtaxa present at the start. Thus the two null hypotheses represent end members of a diversity-independent/diversity-dependent continuum of possibilities.Detailed analyses using the evolutionary bootstrap, in conjunction with the clade statistics of Gould et al. (1977), show that several of the 17 higher taxa studied have diversity histories that are statistically significantly different from the random expectation under one or both null hypotheses. Analyses of multiple taxa in aggregate also reveal several properties of diversity histories that are statistically significantly different from random. Real taxa tend to have higher uniformities and lower maximum diversities than expected under the multiplicative null hypothesis. They have lower uniformities, higher maximum diversities, and longer durations than expected under the additive null hypothesis. And, they have lower centers of gravity than expected under either null hypothesis. Overall, the results provide a possible statistical verification of the process of taxonomic (traditionally, adaptive) radiation and suggest the need to consider deterministic explanations for observed diversity patterns.

Effect of Fixture Compliance on Thermally Enhanced Edge Registration in Microlamination

2004 ◽  
Vol 126 (4) ◽  
pp. 845-848 ◽  
Author(s):  
Wassanai Wattanutchariya ◽  
Brian K. Paul
Keyword(s):  
Thermal Expansion ◽  
Theoretical Model ◽  
Diffusion Bonding ◽  
Tolerance Limit ◽  
Thin Layers ◽  
New Approach ◽  
Large Numbers ◽  
Buckling Behavior ◽  
Differential Thermal Expansion ◽  
Bulk Processing

Microlamination involves the patterning, registration, and bonding of thin layers of material, called laminae, to produce highly paralleled, spatially intensified microchannel systems for the bulk processing of mass and energy. A Thermally Enhanced Edge Registration (TEER) technique has been developed for precision aligning large numbers of laminae in diffusion-bonding processes based on the differential thermal expansion between the laminae and bonding fixture. However, fixture tolerances necessary to promote buckle-free TEER bonding have been found to be very small (below 10 μm). This research focuses on the development of a new approach to thermal registration based on fixture compliance to permit looser fixture tolerances. An analysis based on both fin-buckling behavior and the compliance of the fixture is implemented to investigate the tolerance limit of a compliant TEER fixture. Experiments are conducted to verify the theoretical model. Results show that a compliant fixture can permit an acceptable tolerance limit in TEER.

scholarly journals "The Generative Role of Settlement Aggregation and Urbanization"

2017 ◽  
Author(s):  
Michael E. Smith
Keyword(s):  
Community Formation ◽  
New Approach ◽  
Settlement Systems ◽  
The Past ◽  
Theoretical Support ◽  
Large Numbers ◽  
The Social ◽  
Demographic Processes ◽  
Model Aggregation ◽  
Scalar Stress

: I describe a new approach to understanding processes of village aggregation and urbanization in the past. The key concept—energized crowding—refers to the social effects of large numbers of social interactions that take place within settlements. Demographic processes of population growth and settlement nucleation (aggregation and urbanization) lead to increased energized crowding, which in turn generates a variety of social outcomes. I discuss those outcomes under three headings: scalar stress, community formation, and economic growth. In this model, aggregation and urbanization are crucial processes that lead—by way of energized crowding—to many documented social outputs in both contemporary and past settlement systems. Because this is a new approach for archaeology, conceptual tools for understanding these processes must be borrowed from other social sciences. In particular, recent research on settlement scaling provides empirical and theoretical support for the notion that aggregation and urbanization were of fundamental importance in generating social change in the past.

A new approach to fracture toughness analysis and its application to ABS polymers

1991 ◽  
Vol 6 (6) ◽  
pp. 1369-1373 ◽  
Author(s):  
Beta Yuhong Ni ◽  
Tong-Yi Zhang ◽  
J.C.M. Li
Keyword(s):  
Fracture Toughness ◽  
Crack Length ◽  
Fracture Behavior ◽  
Unit Area ◽  
Unit Length ◽  
Horizontal Line ◽  
New Approach ◽  
Surface Versus ◽  
Crack Tip Plasticity ◽  
Fractured Surface

A new approach is proposed to analyze the fracture behavior with crack tip plasticity by the use of three independent measurements: E0 is the energy required per unit length of crack front to prepare the crack just before propagation; the Ef-curve is a plot of the energy required to produce a unit area of fractured surface versus the crack length; and the Ka-curve is a plot of the applied stress intensity factor KIapp versus the crack length. For ABS polymers, the prefracture energy E0 is 33 Jm−1; the Ef-curve is a horizontal line of 5.2 × 104 Jm−2; and the Ka curve has three different regions which depend on the development of the plastic zone during fracture.

scholarly journals On the Dispersive Ordering and Applications

2013 ◽  
Vol 2013 ◽  
pp. 1-5
Author(s):  
Tran Loc Hung ◽  
Nguyen Van Son
Keyword(s):  
Unbiased Estimator ◽  
Probability Distributions ◽  
Random Variables ◽  
New Approach ◽  
Laws Of Large Numbers ◽  
Large Numbers ◽  
Dispersive Ordering

The purpose of this paper is to present some results related to the dispersive ordering of probability distributions via dispersion functions of the ℒ1-random variables. A new approach to the Laws of Large Numbers in ℒ1-norm can be applied via received results. A new concept on minimum-dispersive unbiased estimator is considered, too.

scholarly journals Reproducibly sampling SARS-CoV-2 genomes across time, geography, and viral diversity

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 657 ◽  
Author(s):  
Evan Bolyen ◽  
Matthew R. Dillon ◽  
Nicholas A. Bokulich ◽  
Jason T. Ladner ◽  
Brendan B. Larsen ◽  
...  
Keyword(s):  
Software Package ◽  
Tracking System ◽  
Viral Diversity ◽  
Data Provenance ◽  
Time Geography ◽  
Viral Genomes ◽  
Genomic Epidemiology ◽  
Rapid Accumulation ◽  
Support Evaluation ◽  
Random Sampling Approach

The COVID-19 pandemic has led to a rapid accumulation of SARS-CoV-2 genomes, enabling genomic epidemiology on local and global scales. Collections of genomes from resources such as GISAID must be subsampled to enable computationally feasible phylogenetic and other analyses. We present genome-sampler, a software package that supports sampling collections of viral genomes across multiple axes including time of genome isolation, location of genome isolation, and viral diversity. The software is modular in design so that these or future sampling approaches can be applied independently and combined (or replaced with a random sampling approach) to facilitate custom workflows and benchmarking. genome-sampler is written as a QIIME 2 plugin, ensuring that its application is fully reproducible through QIIME 2’s unique retrospective data provenance tracking system. genome-sampler can be installed in a conda environment on macOS or Linux systems. A complete default pipeline is available through a Snakemake workflow, so subsampling can be achieved using a single command. genome-sampler is open source, free for all to use, and available at https://caporasolab.us/genome-sampler. We hope that this will facilitate SARS-CoV-2 research and support evaluation of viral genome sampling approaches for genomic epidemiology.

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