A hierarchical Bayesian mixture model for inferring the expression state of genes in transcriptomes.

Transcriptomes are key to understanding the relationship between genotype and phenotype. The ability to infer the expression state (active or inactive) of genes in the transcriptome offers unique benefits for addressing this issue. For example, qualitative changes in gene expression may underly the origin of novel phenotypes, and expression states are readily comparable between tissues and species.

A Bayesian Approach for Inferring the Impact of a Discrete Character on Rates of Continuous-Character Evolution in the Presence of Background-Rate Variation.

Understanding how and why rates of character evolution vary across the Tree of Life is central to many evolutionary questions; for example, does the trophic apparatus (a set of continuous characters) evolve at a higher rate in fish lineages that dwell in reef versus nonreef habitats (a discrete character)? Existing approaches for inferring the relationship between a discrete character and rates of continuous-character evolution rely on comparing a null model (in which rates of continuous-character evolution are constant across lineages) to an alternative model (in which rates of continuous-character evolution depend on the state of the discrete character under consideration). However, these approaches are susceptible to a "straw-man" effect: the influence of the discrete character is inflated because the null model is extremely unrealistic. Here, we describe MuSSCRat, a Bayesian approach for inferring the impact of a discrete trait on rates of continuous-character evolution in the presence of alternative sources of rate variation ("background-rate variation").

Rapid Global Spread of wRi-like Wolbachia across Multiple Drosophila.

Maternally transmitted Wolbachia, Spiroplasma, and Cardinium bacteria are common in insects [1], but their interspecific spread is poorly understood. Endosymbionts can spread rapidly within host species by manipulating host reproduction, as typified by the global spread of wRi Wolbachia observed in Drosophila simulans [2, 3]. However, because Wolbachia cannot survive outside host cells, spread between distantly related host species requires horizontal transfers that are presumably rare [4-7].

RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language.

Programs for Bayesian inference of phylogeny currently implement a unique and fixed suite of models. Consequently, users of these software packages are simultaneously forced to use a number of programs for a given study, while also lacking the freedom to explore models that have not been implemented by the developers of those programs. We developed a new open-source software package, RevBayes, to address these problems.

How Well Can We Detect Lineage-Specific Diversification-Rate Shifts? A Simulation Study of Sequential AIC Methods.

Evolutionary biologists have long been fascinated by the extreme differences in species numbers across branches of the Tree of Life. This has motivated the development of statistical methods for detecting shifts in the rate of lineage diversification across the branches of phylogenic trees. One of the most frequently used methods, MEDUSA, explores a set of diversification-rate models, where each model assigns branches of the phylogeny to a set of diversification-rate categories.

TESS: an R package for efficiently simulating phylogenetic trees and performing Bayesian inference of lineage diversification rates.

Unlabelled: Many fundamental questions in evolutionary biology entail estimating rates of lineage diversification (speciation-extinction) that are modeled using birth-death branching processes. We leverage recent advances in branching-process theory to develop a flexible Bayesian framework for specifying diversification models-where rates are constant, vary continuously, or change episodically through time-and implement numerical methods to estimate parameters of these models from molecular phylogenies, even when species sampling is incomplete. We enable both statistical inference and efficient simulation under these models.

Phylodynamics of H5N1 Highly Pathogenic Avian Influenza in Europe, 2005-2010: Potential for Molecular Surveillance of New Outbreaks.

Previous Bayesian phylogeographic studies of H5N1 highly pathogenic avian influenza viruses (HPAIVs) explored the origin and spread of the epidemic from China into Russia, indicating that HPAIV circulated in Russia prior to its detection there in 2005. In this study, we extend this research to explore the evolution and spread of HPAIV within Europe during the 2005-2010 epidemic, using all available sequences of the hemagglutinin (HA) and neuraminidase (NA) gene regions that were collected in Europe and Russia during the outbreak. We use discrete-trait phylodynamic models within a Bayesian statistical framework to explore the evolution of HPAIV.

The dawn of open access to phylogenetic data.

The scientific enterprise depends critically on the preservation of and open access to published data. This basic tenet applies acutely to phylogenies (estimates of evolutionary relationships among species). Increasingly, phylogenies are estimated from increasingly large, genome-scale datasets using increasingly complex statistical methods that require increasing levels of expertise and computational investment.

A critical appraisal of the use of microRNA data in phylogenetics.

Recent progress in resolving the tree of life continues to expose relationships that resist resolution, which drives the search for novel sources of information to solve these difficult phylogenetic problems. A recent example, the presence and absence of microRNA families, has been vigorously promoted as an ideal source of phylogenetic data and has been applied to several perennial phylogenetic problems. The utility of such data for phylogenetic inference hinges critically both on developing stochastic models that provide a reasonable description of the process that give rise to these data, and also on the careful validation of those models in real inference scenarios.

Heterostyly accelerates diversification via reduced extinction in primroses.

The exceptional species diversity of flowering plants, exceeding that of their sister group more than 250-fold, is especially evident in floral innovations, interactions with pollinators and sexual systems. Multiple theories, emphasizing flower-pollinator interactions, genetic effects of mating systems or high evolvability, predict that floral evolution profoundly affects angiosperm diversification. However, consequences for speciation and extinction dynamics remain poorly understood.

Bayesian analysis of biogeography when the number of areas is large.

Historical biogeography is increasingly studied from an explicitly statistical perspective, using stochastic models to describe the evolution of species range as a continuous-time Markov process of dispersal between and extinction within a set of discrete geographic areas. The main constraint of these methods is the computational limit on the number of areas that can be specified. We propose a Bayesian approach for inferring biogeographic history that extends the application of biogeographic models to the analysis of more realistic problems that involve a large number of areas.

Pediatric observation units.

Pediatric observation units (OUs) are hospital areas used to provide medical evaluation and/or management for health-related conditions in children, typically for a well-defined, brief period. Pediatric OUs represent an emerging alternative site of care for selected groups of children who historically may have received their treatment in an ambulatory setting, emergency department, or hospital-based inpatient unit. This clinical report provides an overview of pediatric OUs, including the definitions and operating characteristics of different types of OUs, quality considerations and coding for observation services, and the effect of OUs on inpatient hospital utilization.

Dispensing medications at the hospital upon discharge from an emergency department.

Although most health care services can and should be provided by their medical home, children will be referred or require visits to the emergency department (ED) for emergent clinical conditions or injuries. Continuation of medical care after discharge from an ED is dependent on parents or caregivers' understanding of and compliance with follow-up instructions and on adherence to medication recommendations. ED visits often occur at times when the majority of pharmacies are not open and caregivers are concerned with getting their ill or injured child directly home.

A Bayesian approach for evaluating the impact of historical events on rates of diversification.

Evolutionary biologists often wish to explore the impact of a particular historical event (e.g., the origin of a novel morphological trait, an episode of biogeographic dispersal, or the onset of an ecological association) on rates of diversification (speciation minus extinction).

Language barriers as a reported cause of prehospital care delay in Minnesota.

Objective: Although anecdotal reports exist, the frequency of language barriers encountered between EMS providers and patients/families in the prehospital environment remains unknown. The purpose of this study was to determine the frequency of EMS provider-reported perceived delays in care due to language barrier and to characterize the nature of calls involved.

Methods: Retrospective analysis of the Minnesota State Ambulance Reporting system (MNSTAR) database, a mandated statewide EMS data collection tool.

Correlates of diversification in the plant clade Dipsacales: geographic movement and evolutionary innovations.

We explore patterns of diversification in the plant clades Adoxaceae and Valerianaceae (within Dipsacales), evaluating correlations between biogeographic change (i.e., movements into new areas), morphological change (e.

Increasing data transparency and estimating phylogenetic uncertainty in supertrees: Approaches using nonparametric bootstrapping.

The estimation of ever larger phylogenies requires consideration of alternative inference strategies, including divide-and-conquer approaches that decompose the global inference problem to a set of smaller, more manageable component problems. A prominent locus of research in this area is the development of supertree methods, which estimate a composite tree by combining a set of partially overlapping component topologies. Although promising, the use of component tree topologies as the primary data dissociates supertrees from complexities within the underling character data and complicates the evaluation of phylogenetic uncertainty.

A likelihood framework for inferring the evolution of geographic range on phylogenetic trees.

At a time when historical biogeography appears to be again expanding its scope after a period of focusing primarily on discerning area relationships using cladograms, new inference methods are needed to bring more kinds of data to bear on questions about the geographic history of lineages. Here we describe a likelihood framework for inferring the evolution of geographic range on phylogenies that models lineage dispersal and local extinction in a set of discrete areas as stochastic events in continuous time. Unlike existing methods for estimating ancestral areas, such as dispersal-vicariance analysis, this approach incorporates information on the timing of both lineage divergences and the availability of connections between areas (dispersal routes).

Pediatric emergencies on a US-based commercial airline.

Objectives: The purpose of this investigation was to determine the incidence and character of pediatric emergencies on a US-based commercial airline and to evaluate current in-flight medical kits.

Methods: In-flight consultations to a major US airline by a member of our staff are recorded in an institutional database. In this observational retrospective review, the database was queried for consultations for all passengers up to 18 years old between January 1, 1995, and December 31, 2002.

Performance of a decision rule for radiographs of pediatric knee injuries.

Although decision rules for radiographs of pediatric knee injuries have been suggested from retrospective studies, prospective evaluations of such rules have been limited. We sought to prospectively assess the performance of a rule in children presenting with acute knee injuries. Eligible participants were children aged 3-18 years with an acute knee injury.