8 Works

Data from: The neuropathic diabetic foot ulcer microbiome is associated with clinical factors.

Sue E. Gardner, Stephen L. Hillis, Kris Heilmann, Julia A. Segre & Elizabeth A. Grice
Nonhealing diabetic foot ulcers (DFUs) are a common and costly complication of diabetes. Microbial burden, or "bioburden," is believed to underlie delayed healing, although little is known of those clinical factors that may influence microbial load, diversity, and/or pathogenicity. We profiled the microbiomes of neuropathic nonischemic DFUs without clinical evidence of infection in 52 individuals using high-throughput sequencing of the bacterial 16S ribosomal RNA gene. Comparatively, wound cultures, the standard diagnostic in the clinic, vastly...

Data from: Inferring heterogeneous evolutionary processes through time: from sequence substitution to phylogeography

Filip Bielejec, Philippe Lemey, Guy Baele, Andrew Rambaut & Marc A. Suchard
Molecular phylogenetic and phylogeographic reconstructions generally assume time-homogeneous substitution processes. Motivated by computational convenience, this assumption sacrifices biological realism and offers little opportunity to uncover the temporal dynamics in evolutionary histories. Here, we propose an evolutionary approach that explicitly relaxes the time-homogeneity assumption by allowing the specification of different infinitesimal substitution rate matrices across different time intervals, called epochs, along the evolutionary history. We focus on an epoch model implementation in a Bayesian inference framework...

Data from: Maternal effects and population regulation: maternal density-induced reproduction suppression impairs offspring capacity in response to immediate environment in root voles Microtus oeconomus

Jiang-Hui Bian, Shou-Yang Du, Yan Wu, Yi-Fan Cao, Xu-Heng Nie, Hui He & Zhi-Bing You
1. The hypothesis that maternal effects act as an adaptive bridge in translating maternal environments into offspring phenotypes and thereby affecting population dynamics has not been studied in the well-controlled fields. 2. In this study, the effects of maternal population-density on offspring stress axis, reproduction and population dynamics were studied in root voles (Microtus oeconomus). Parental enclosures for breeding offspring were established by introducing 6 adults per sex into each of 4 (low density) and...

Data from: Integrating influenza antigenic dynamics with molecular evolution

Trevor Bedford, Marc A. Suchard, Philippe Lemey, Gytis Dudas, Victoria Gregory, Alan J. Hay, John W. McCauley, Colin A. Russell, Derek J. Smith & Andrew Rambaut
Influenza viruses undergo continual antigenic evolution allowing mutant viruses to evade host immunity acquired to previous virus strains. Antigenic phenotype is often assessed through pairwise measurement of cross-reactivity between influenza strains using the hemagglutination inhibition (HI) assay. Here, we extend previous approaches to antigenic cartography, and simultaneously characterize antigenic and genetic evolution by modeling the diffusion of antigenic phenotype over a shared virus phylogeny. Using HI data from influenza lineages A/H3N2, A/H1N1, B/Victoria and B/Yamagata,...

Data from: Sexually coercive male chimpanzees sire more offspring

Joseph T. Feldblum, Emily E. Wroblewski, Rebecca S. Rudicell, Beatrice H. Hahn, Thais Paiva, Mine Cetinkaya-Rundel, Anne E. Pusey & Ian C. Gilby
In sexually reproducing animals, male and female reproductive strategies often conflict. In some species, males use aggression to overcome female choice, but debate persists over the extent to which this strategy is successful. Previous studies of male aggression toward females among wild chimpanzees have yielded contradictory results about the relationship between aggression and mating behavior. Critically, however, copulation frequency in primates is not always predictive of reproductive success. We analyzed a 17-year sample of behavioral...

Data from: Understanding genetic variation in in vivo tolerance to artesunate: implications for treatment efficacy and resistance monitoring

Laura C. Pollitt, Derek Sim, Rahel Salathé & Andrew F. Read
Artemisinin-based drugs are the front-line weapon in the treatment of human malaria cases, but there is concern that recent reports of slow clearing infections may signal developing resistance to treatment. In the absence of molecular markers for resistance, current efforts to monitor drug efficacy are based on the rate at which parasites are cleared from infections. However, some knowledge of the standing variation in parasite susceptibility is needed to identify a meaningful increase in infection...

Data from: Adaptive evolution and environmental durability jointly structure phylodynamic patterns in avian influenza viruses

Benjamin Roche, John M. Drake, Justin Brown, David E. Stallknecht, Trevor Bedford & Pejman Rohani
Avian influenza viruses (AIVs) have been pivotal to the origination of human pandemic strains. Despite their scientific and public health significance, however, there remains much to be understood about the ecology and evolution of AIVs in wild birds, where major pools of genetic diversity are generated and maintained. Here, we present comparative phylodynamic analyses of human and AIVs in North America, demonstrating (i) significantly higher standing genetic diversity and (ii) phylogenetic trees with a weaker...

Data from: Global distribution maps of the Leishmaniases

David M. Pigott, Samir Bhatt, Nick Golding, Kirsten A. Duda, Katherine E. Battle, Oliver J. Brady, Jane P. Messina, Yves Balard, Patrick Bastien, Francine Pratlong, John S. Brownstein, Clark C Freifeld, Sumiko R. Mekaru, Peter W. Gething, Dylan B. George, Monica F. Myers, Richard Reithinger & Simon I. Hay
The leishmaniases are vector-borne diseases that have a broad global distribution throughout much of the Americas, Africa and Asia. Despite representing a significant public health burden, our understanding of the global distribution of the leishmaniases remains vague, reliant upon expert opinion and limited to poor spatial resolution. A global assessment of the consensus of evidence for leishmaniasis was performed at a sub-national level by aggregating information from a variety of sources. A database of records...

Registration Year

  • 2014

Resource Types

  • Dataset


  • National Institutes of Health
  • University of Edinburgh
  • University of Pennsylvania
  • University of California Los Angeles
  • KU Leuven
  • Fred Hutchinson Cancer Research Center
  • University of Michigan-Ann Arbor
  • David Geffen School of Medicine at UCLA
  • Duke University
  • University of Georgia