Popliteal artery entrapment syndrome

This issue of eMedRef provides information to clinicians on the pathophysiology, diagnosis, and therapeutics of popliteal artery entrapment syndrome

The plenary address: A rhetorical analysis

In terms of structure, style, content and intended audience, Genre Analysis 58, this thesis presents a rhetorical analysis of the plenary address as a genre. Four examples of the opening plenary were analyzed because they represent the opening plenary lecture-keynote speech type, the most common presented at conferences: Mina Shaughnessy and the teaching of writing, Keynote address, Literacy after the revolution and The uneasy partnership between grammar and writing instruction

The Expansion of Class Concepts and the Colorado Coal Field War Project

The Colorado Coal Field War Project was an attempt by McGuire, Reckner, and others to develop a \u27working-class\u27 archaeology that served the public as well as the archaeologists performing excavations and research. The attempt was successful, promoting and supporting ideas that had been discussed in archaeology about gender, class, and the treatment of archaeology as a craft. Their example of using archaeology to benefit communities as well as academic interests can and should be tested in other regions of the United States as well as the rest of the world

The Expansion of Class Concepts and the Colorado Coal Field War Project

The Colorado Coal Field War Project was an attempt by McGuire, Reckner, and others to develop a \u27working-class\u27 archaeology that served the public as well as the archaeologists performing excavations and research. The attempt was successful, promoting and supporting ideas that had been discussed in archaeology about gender, class, and the treatment of archaeology as a craft. Their example of using archaeology to benefit communities as well as academic interests can and should be tested in other regions of the United States as well as the rest of the world

tRNA signatures reveal polyphyletic origins of streamlined SAR11 genomes among the alphaproteobacteria

Phylogenomic analyses are subject to bias from compositional convergence and noise from horizontal gene transfer (HGT). Compositional convergence is a likely cause of controversy regarding phylogeny of the SAR11 group of Alphaproteobacteria that have extremely streamlined, A+T-biased genomes. While careful modeling can reduce artifacts caused by convergence, the most consistent and robust phylogenetic signal in genomes may lie distributed among encoded functional features that govern macromolecular interactions. Here we develop a novel phyloclassification method based on signatures derived from bioinformatically defined tRNA Class-Informative Features (CIFs). tRNA CIFs are enriched for features that underlie tRNA-protein interactions. Using a simple tRNA-CIF-based phyloclassifier, we obtained results consistent with those of bias-corrected whole proteome phylogenomic studies, rejecting monophyly of SAR11 and affiliating most strains with Rhizobiales with strong statistical support. Yet SAR11 and Rickettsiales tRNA genes share distinct patterns of A+T-richness, as expected from their elevated genomic A+T compositions. Using conventional supermatrix methods on total tRNA sequence data, we could recover the artifactual result of a monophyletic SAR11 grouping with Rickettsiales. Thus tRNA CIF-based phyloclassification is more robust to base content convergence than supermatrix phylogenomics on whole tRNA sequences. Also, given the notoriously promiscuous HGT of aminoacyl-tRNA synthetases, tRNA CIF-based phyloclassification may be relatively robust to HGT of network components. We describe how unique features of tRNA-protein interaction networks facilitate the mining of traits governing macromolecular interactions from genomic data, and discuss why interaction-governing traits may be especially useful to solve difficult problems in microbial classification and phylogeny

tRNA functional signatures classify plastids as late-branching cyanobacteria.

BackgroundEukaryotes acquired the trait of oxygenic photosynthesis through endosymbiosis of the cyanobacterial progenitor of plastid organelles. Despite recent advances in the phylogenomics of Cyanobacteria, the phylogenetic root of plastids remains controversial. Although a single origin of plastids by endosymbiosis is broadly supported, recent phylogenomic studies are contradictory on whether plastids branch early or late within Cyanobacteria. One underlying cause may be poor fit of evolutionary models to complex phylogenomic data.ResultsUsing Posterior Predictive Analysis, we show that recently applied evolutionary models poorly fit three phylogenomic datasets curated from cyanobacteria and plastid genomes because of heterogeneities in both substitution processes across sites and of compositions across lineages. To circumvent these sources of bias, we developed CYANO-MLP, a machine learning algorithm that consistently and accurately phylogenetically classifies ("phyloclassifies") cyanobacterial genomes to their clade of origin based on bioinformatically predicted function-informative features in tRNA gene complements. Classification of cyanobacterial genomes with CYANO-MLP is accurate and robust to deletion of clades, unbalanced sampling, and compositional heterogeneity in input tRNA data. CYANO-MLP consistently classifies plastid genomes into a late-branching cyanobacterial sub-clade containing single-cell, starch-producing, nitrogen-fixing ecotypes, consistent with metabolic and gene transfer data.ConclusionsPhylogenomic data of cyanobacteria and plastids exhibit both site-process heterogeneities and compositional heterogeneities across lineages. These aspects of the data require careful modeling to avoid bias in phylogenomic estimation. Furthermore, we show that amino acid recoding strategies may be insufficient to mitigate bias from compositional heterogeneities. However, the combination of our novel tRNA-specific strategy with machine learning in CYANO-MLP appears robust to these sources of bias with high accuracy in phyloclassification of cyanobacterial genomes. CYANO-MLP consistently classifies plastids as late-branching Cyanobacteria, consistent with independent evidence from signature-based approaches and some previous phylogenetic studies