Publications by authors named "Featherstone L"

Phylogenetic analyses are crucial for understanding microbial evolution and infectious disease transmission. Bacterial phylogenies are often inferred from SNP alignments, with SNPs as the fundamental signal within these data. SNP alignments can be reduced to a 'strict core' by removing those sites that do not have data present in every sample.

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There is an increasing number of libraries devoted to parsing, manipulating and visualising phylogenetic trees in JavaScript. Many of these libraries bundle tree manipulation with visualisation, but have limited ability to manipulate trees and lack detailed documentation. As the number of web-based phylogenetic tools and the size of phylogenetics datasets increases, there is a need for a library that parses, writes and manipulates phylogenetic trees that is interoperable with other phylogenetic and data visualisation libraries.

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Sequence capture is a genomic technique that selectively enriches target sequences before high throughput next-generation sequencing, to generate specific sequences of interest. Off-target or 'bycatch' data are often discarded from capture experiments, but can be leveraged to address evolutionary questions under some circumstances. Here, we investigated the effects of missing data on a variety of evolutionary analyses using bycatch from an exon capture experiment on the global pest moth, Helicoverpa armigera.

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Article Synopsis
  • Molecular sequence data from rapidly evolving organisms can be sampled at different times, which helps in calibrating molecular clocks using root-to-tip (RTT) regression.
  • Clockor2 is a new web application designed for efficient RTT regression, allowing users to quickly fit both local and global molecular clocks, even with complex genomic datasets.
  • The application processes data on the client-side for enhanced speed and privacy, handling large datasets with trees of up to 10,000 tips, and is available for free online.
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Inferring the spatiotemporal spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) via Bayesian phylogeography has been complicated by the overwhelming sampling bias present in the global genomic dataset. Previous work has demonstrated the utility of metadata in addressing this bias. Specifically, the inclusion of recent travel history of SARS-CoV-2-positive individuals into extended phylogeographical models has demonstrated increased accuracy of estimates, along with proposing alternative hypotheses that were not apparent using only genomic and geographical data.

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Despite its increasing role in the understanding of infectious disease transmission at the applied and theoretical levels, phylodynamics lacks a well-defined notion of ideal data and optimal sampling. We introduce a method to visualize and quantify the relative impact of pathogen genome sequence and sampling times-two fundamental sources of data for phylodynamics under birth-death-sampling models-to understand how each drives phylodynamic inference. Applying our method to simulated data and real-world SARS-CoV-2 and H1N1 Influenza data, we use this insight to elucidate fundamental trade-offs and guidelines for phylodynamic analyses to draw the most from sequence data.

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The historical epidemiology of plague is controversial due to the scarcity and ambiguity of available data. A common source of debate is the extent and pattern of plague re-emergence and local continuity in Europe during the 14th-18th century CE. Despite having a uniquely long history of plague (∼5,000 years), Scandinavia is relatively underrepresented in the historical archives.

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Plague has an enigmatic history as a zoonotic pathogen. This infectious disease will unexpectedly appear in human populations and disappear just as suddenly. As a result, a long-standing line of inquiry has been to estimate when and where plague appeared in the past.

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Phylodynamics requires an interdisciplinary understanding of phylogenetics, epidemiology, and statistical inference. It has also experienced more intense application than ever before amid the SARS-CoV-2 pandemic. In light of this, we present a review of phylodynamic models beginning with foundational models and assumptions.

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We explored how the duration, size, and number of virus transmission clusters, defined as country-specific monophyletic groups in a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) phylogenetic tree, differed among the Nordic countries of Norway, Sweden, Denmark, Finland, and Iceland. Our results suggest that although geographical connectivity, population density, and openness influence the spread and the size of SARS-CoV-2 transmission clusters, the different country-specific intervention strategies had the largest impact. We also found a significant positive association between the size and duration of transmission clusters in the Nordic countries, suggesting that the rapid deployment of contact tracing is a key response measure in reducing virus transmission.

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Article Synopsis
  • Many countries used non-pharmaceutical interventions to control COVID-19 and reduce movement and contact, but the effects on the spread of the virus (SARS-CoV-2) remain unclear.
  • The study analyzed complete SARS-CoV-2 genomes from Denmark, Finland, Iceland, Norway, and Sweden to understand virus transmission and exportation during the first year of the pandemic.
  • The research found that differing strategies, particularly Sweden's reliance on recommendations rather than strict laws, led to increased transmission and spread of the virus, demonstrating the importance of genomic surveillance in monitoring virus transmission dynamics.
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The ongoing SARS-CoV-2 outbreak marks the first time that large amounts of genome sequence data have been generated and made publicly available in near real time. Early analyses of these data revealed low sequence variation, a finding that is consistent with a recently emerging outbreak, but which raises the question of whether such data are sufficiently informative for phylogenetic inferences of evolutionary rates and time scales. The phylodynamic threshold is a key concept that refers to the point in time at which sufficient molecular evolutionary change has accumulated in available genome samples to obtain robust phylodynamic estimates.

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This paper will explore the constructions of white male sexuality in late nineteenth-century Australia by the medical profession. In a period where female sexuality was always suspect, male sexuality, too, was brought into question, and the male body was increasingly constructed as vulnerable to sexual excess and sexual pathology. If male sexuality was to be active and dynamic, this could readily go too far, rendering men merely a slip away from deviance.

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Between 1880 and 1910 paediatrics in Australia developed not merely as a response to Enlightenment philosophical understandings of the child as precious and special, but as part of a wider demand for reproduction and population. A brief sketch of the international context will situate the specific Australian conditions, which include education, professionalisation and the emerging concept of infant mortality. A level of general specialisation within medicine was necessary for the development of paediatrics, in addition to a general and new interest in child health, which was a response to the social, political and economic needs of the emerging nation.

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Coaggregation between Porphyromonas gingivalis and Fusobacterium nucleatum strains was previously studied using either a semi-quantitative macroscopic assay or radioactive tracer assays. A new automated microtiter plate assay is introduced, in which the plate reader (Vmax) was adapted to allow quantitative evaluation of the kinetics of coaggregation. F nucleatum PK 1594 coaggregated with P.

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Background: Congenital complete heart block is an uncommon fetal arrhythmia characterized by complete dissociation of the atrial and ventricular contractions.

Cases: Two patients were diagnosed with isolated congenital complete heart block in the second trimester of pregnancy. Successful vaginal delivery was achieved by both.

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Lysine and S(2-aminoethyl)cysteine (AEC) metabolism were investigated in normal barley (Hordeum vulgare L. cv. Bomi) and a hemozygous recessive AEC-resistant mutant (R906).

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