Biomedical subjects

Brian R Moore

Publications and source records attributed to Brian R Moore.

7 recordsLinked to original sources

PubMed2006

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. We address these issues by exploring three approaches that variously incorporate nonparametric bootstrapping into a common supertree estimation algorithm (matrix representation with parsimony, although any algorithm might be used), including bootstrap-weighting, source-tree bootstrapping, and hierarchical bootstrapping. We illustrate these procedures by means of hypothetical and empirical examples. Our preliminary experiments suggest that these methods have the potential to improve the correspondence of supertree estimates to those derived from simultaneous analysis of the combined data and to allow uncertainty in supertree topologies to be quantified. The ability to increase the transparency of supertrees to the underlying character data has several practical implications and sheds new light on an old debate. These methods have been implemented in the freely available program, tREeBOOT.

Classification↗

PubMed2005

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. The settings for the study were a tertiary pediatric emergency department (ED), a community hospital ED, and a pediatric urgent care center. All of the participants received standard knee radiographs. Before radiography, each patient was assessed by a pediatrician or pediatric emergency physician for presence of the following: 1) inability to bear weight, 2) inability to flex the knee to 90( degrees ), 3) presence of bony tenderness. The radiographs were interpreted by a radiologist blinded to the study; those with findings reported as consistent with acute fracture were considered positive. A total of 146 patients were enrolled (65% male, mean age 11.6 years). Of these, 15 (10.3%) had a fracture on their radiograph, 6 of which were related to trampoline use. Seventy-seven (53%) were negative for criterion 1 (i.e., able to bear weight immediately after the accident and in the ED), none (0%) of whom had fractures. The negative predictive value of this criterion was 1.0 (95% CI 0.94-1.0). The positive predictive value was 0.22 (95% CI 0.13-0.34). The sensitivity was 1.0 (95% CI 0.82-1.0). The specificity was 0.59 (95% CI 0.50-0.67). Three patients negative for criterion 3 were found to have fractures. The proximal tibia was the most common fracture site (47%). In conclusion, assessment of the ability to bear weight would have decreased the use of radiography by 53% without missing any fractures in our study population. No additional value to the rule was found by adding assessment of the ability to flex the knee or bony tenderness.

Adolescent↗

PubMed2005

A reexamination of the feasibility of the administration of routine childhood vaccines in emergency departments in the era of electronic vaccine registries.

OBJECTIVES: To determine if electronic vaccine records facilitate successful routine childhood vaccination in the emergency department (ED). METHODS: We sampled consecutively over 2 calendar months children younger than 24 months presenting to the ED. Parents and legal guardians of eligible children were offered enrollment. Those consenting completed a parental survey after a nurse conducted an initial assessment of eligibility. Attending physicians then completed the assessment, and after the visit, the electronic vaccination records, when available, were accessed. No actual routine childhood vaccines were given during the study. RESULTS: Three hundred thirty-four were approached: 17 (5.1%) declined participation; 10 (3.0%) were enrolled, but the data were lost, and 7 (2.1%) were excluded. Of the 300 remaining, 235 (78.3%) had available electronic vaccine records. Only 38 (16.2%) of the 235 were late for at least 1 vaccine. Of note, physicians assessed 22 (57.9%) of the 38 as medically appropriate for vaccination in the ED. The overwhelming majority (81.8%) of the 22 parents and guardians would have assented to vaccination in the ED. Of the 38 patients found late for vaccination, 31 (81.6%) of parents incorrectly reported their children to be up-to-date on their immunizations. CONCLUSIONS: Assuming that the electronic vaccination record performed such as an online vaccine registry, the effort to access the registry might find a substantial number of children late for a routine childhood vaccination. In this setting, we found that approximately one sixth of the children with electronic vaccine records would be found late for vaccination, and based on physician assessment and parental survey, one half of those children would receive that vaccination if available in the ED. These rates offer health care planners a sense of the magnitude of the vaccination rates in the ED as we move toward regional vaccination registries with online capabilities to be accessed by EDs.

Emergency Service, Hospital↗

PubMed2005

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. Consultations were reviewed for type of emergency, use of the medical kit, and unscheduled landings. RESULTS: Two hundred twenty-two pediatric consultations were identified, representing 1 pediatric call per 20,775 flights. The mean age of patients was 6.8 years. Fifty-three emergencies were preflight calls, and 169 were in-flight pediatric consultations. The most common in-flight consultations concerned infectious disease (45 calls, 27%), neurological (25 calls, 15%), and respiratory tract (22 calls, 13%) emergencies. The emergency medical kit was used for 60 emergencies. Nineteen consultations (11%) resulted in flight diversions (1/240,000 flights), most commonly because of in-flight neurological (9) and respiratory tract (5) emergencies. International flights had a higher incidence than domestic flights of consultations and diversions for pediatric emergencies. CONCLUSIONS: The most common in-flight pediatric emergencies involved infectious diseases and neurological and respiratory tract problems. Emergency medical kits should be expanded to include pediatric medications.

Adolescent↗

PubMed2005

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). Monte Carlo methods are used to estimate branch-specific transition probabilities for geographic ranges, enabling the likelihood of the data (observed species distributions) to be evaluated for a given phylogeny and parameterized paleogeographic model. We demonstrate how the method can be used to address two biogeographic questions: What were the ancestral geographic ranges on a phylogenetic tree? How were those ancestral ranges affected by speciation and inherited by the daughter lineages at cladogenesis events? For illustration we use hypothetical examples and an analysis of a Northern Hemisphere plant clade (Cercis), comparing and contrasting inferences to those obtained from dispersal-vicariance analysis. Although the particular model we implement is somewhat simplistic, the framework itself is flexible and could readily be modified to incorporate additional sources of information and also be extended to address other aspects of historical biogeography.

Biological Evolution↗

PubMed2004

SYMMETREE: whole-tree analysis of differential diversification rates.

UNLABELLED: SymmeTREE implements several tests of differential diversification rates that exploit information on the topological distribution of species diversity throughout entire trees to address two general questions: (1) Has a given tree experienced significant variation in diversification rates among its branches? and (2) If so, along which branches have significant shifts in diversification rate occurred? These explicitly model-based methods are robust to uncertainty in estimates of branch length/duration and can accommodate incompletely resolved trees and other forms of phylogenetic uncertainty. AVAILABILITY: http://www.phylodiversity.net/bmoore/software.html CONTACT: brian.moore@yale.edu.

Algorithms↗

PubMed2002

Whole-tree methods for detecting differential diversification rates.

Prolific cladogenesis, adaptive radiation, species selection, key innovations, and mass extinctions are a few examples of biological phenomena that lead to differential diversification among lineages. Central to the study of differential diversification rates is the ability to distinguish chance variation from that which requires deterministic explanation. To detect diversification rate variation among lineages, we propose a number of methods that incorporate information on the topological distribution of species diversity from all internal nodes of a phylogenetic tree. These whole-tree methods (M(Pi), M(Sigma), and M(R)) are explicitly connected to a null model of random diversification--the equal-rates Markov (ERM) random branching model--and an alternative model of differential diversification: M(Pi) is based on the product of individual nodal ERM probabilities; M(Sigma) is based on the sum of individual nodal ERM probabilities, and M(R) is based on a transformation of ERM probabilities that corresponds to a formalized system that orders trees by their relative symmetry. These methods have been implemented in a freely available computer program, SYMMETREE, to detect clades with variable diversification rates, thereby allowing the study of biological processes correlated with and possibly causal to shifts in diversification rate. Application of these methods to several published phylogenies demonstrates their ability to contend with relatively large, incompletely resolved trees. These topology-based methods do not require estimates of relative branch lengths, which should facilitate the analysis of phylogenies, such as supertrees, for which such data are unreliable or unavailable.

Animals↗