Identification of Upper Respiratory Tract Pathogens Using Electrochemical Detection on an Oligonucleotide Microarray

Bacterial and viral upper respiratory infections (URI) produce highly variable clinical symptoms that cannot be used to identify the etiologic agent. Proper treatment, however, depends on correct identification of the pathogen involved as antibiotics provide little or no benefit with viral infections. Here we describe a rapid and sensitive genotyping assay and microarray for URI identification using standard amplification and hybridization techniques, with electrochemical detection (ECD) on a semiconductor-based oligonucleotide microarray. The assay was developed to detect four bacterial pathogens (Bordetella pertussis, Streptococcus pyogenes, Chlamydia pneumoniae and Mycoplasma pneumoniae) and 9 viral pathogens (adenovirus 4, coronavirus OC43, 229E and HK, influenza A and B, parainfluinza types 1, 2, and 3 and respiratory syncytial virus. This new platform forms the basis for a fully automated diagnostics system that is very flexible and can be customized to suit different or additional pathogens. Multiple probes on a flexible platform allow one to test probes empirically and then select highly reactive probes for further iterative evaluation. Because ECD uses an enzymatic reaction to create electrical signals that can be read directly from the array, there is no need for image analysis or for expensive and delicate optical scanning equipment. We show assay sensitivity and specificity that are excellent for a multiplexed format

Phylogeny and divergence time estimates for the fern genus Azolla (Salviniaceae)

A phylogeny for all extant species of the heterosporous fern genus Azolla is presented here based on more than 5000 base pairs of DNA sequence data from six plastid loci (rbcL, atpB, rps4, trnL-trnF, trnG-trnR, and rps4-trnS). Our results are in agreement with other recent molecular phylogenetic hypotheses that support the monophyly of sections Azolla and Rhizosperma and the proposed relationships within section Azolla. Divergence times are estimated within Azolla using a penalized likelihood approach, integrating data from fossils and DNA sequences. Penalized likelihood analyses estimate a divergence time of 50.7 Ma (Eocene) for the split between sections Azolla and Rhizosperma, 32.5 Ma (Oligocene) for the divergence of Azolla nilotica from A. pinnata within section Rhizosperma, and 16.3 Ma (Miocene) for the divergence of the two lineages within section Azolla (the A. filiculoides + A. rubra lineage from the A. caroliniana + A. microphylla + A. mexicana complex). © 2007 by The University of Chicago. All rights reserved

Evolutionary relationships within the Neotropical, eusporangiate fern genus Danaea (Marattiaceae).

Genera within the eusporangiate fern family Marattiaceae have long been neglected in taxonomic and systematic studies. Here we present the first phylogenetic hypothesis of relationships within the exclusively Neotropical genus Danaea based on a sampling of 60 specimens representing 31 species from various Neotropical sites. We used DNA sequence data from three plastid regions (atpB, rbcL, and trnL-F), morphological characters from both herbarium specimens and live plants observed in the field, and geographical and ecological information to examine evolutionary patterns. Eleven representatives of five other marattioid genera (Angiopteris, Archangiopteris, Christensenia, Macroglossum, and Marattia) were used to root the topology. We identified three well-supported clades within Danaea that are consistent with morphological characters: the "leprieurii" clade (containing species traditionally associated with the name D. elliptica), the "nodosa" clade (containing all species traditionally associated with the name D. nodosa), and the "alata" clade (containing all other species). All three clades are geographically and ecologically widely distributed, but subclades within them show various distribution patterns. Our phylogenetic hypothesis provides a robust framework within which broad questions related to the morphology, taxonomy, biogeography, evolution, and ecology of these ferns can be addressed

The paraphyly of Osmunda is confirmed by phylogenetic analyses of seven plastid loci

To resolve phylogenetic relationships among all genera and subgenera in Osmundaceae, we analyzed over 8,500 characters of DNA sequence data from seven plastid loci (atpA, rbcL, rbcL-accD, rbcL-atpB, rps4-trnS, trnG-trnR, and trnL-trnF). Our results confirm those from earlier anatomical and single-gene (rbcL) studies that suggested Osmunda s.l. is paraphyletic. Osmunda cinnamomea is sister to the remainder of Osmundaceae (Leptopteris, Todea, and Osmunda s.s.). We support the recognition of a monotypic fourth genus, Osmundastrum, to reflect these results. We also resolve subgeneric relationships within Osmunda s.s. and find that subg. Claytosmunda is strongly supported as sister to the rest of Osmunda. A stable, well-supported classification for extant Osmundaceae is proposed, along with a key to all genera and subgenera. © Copyright 2008 by the American Society of Plant Taxonomists

A molecular phylogeny of scaly tree ferns (Cyatheaceae).

Tree ferns recently were identified as the closest sister group to the hyperdiverse clade of ferns, the polypods. Although most of the 600 species of tree ferns are arborescent, the group encompasses a wide range of morphological variability, from diminutive members to the giant scaly tree ferns, Cyatheaceae. This well-known family comprises most of the tree fern diversity (∼500 species) and is widespread in tropical, subtropical, and south temperate regions of the world. Here we investigate the phylogenetic relationships of scaly tree ferns based on DNA sequence data from five plastid regions (rbcL, rbcL-accD IGS, rbcL-atpB IGS, trnG-trnR, and trnL-trnF). A basal dichotomy resolves Sphaeropteris as sister to all other taxa and scale features support these two clades: Sphaeropteris has conform scales, whereas all other taxa have marginate scales. The marginate-scaled clade consists of a basal trichotomy, with the three groups here termed (1) Cyathea (including Cnemidaria, Hymenophyllopsis, Trichipteris), (2) Alsophila sensu stricto, and (3) Gymnosphaera (previously recognized as a section within Alsophila) + A. capensis. Scaly tree ferns display a wide range of indusial structures, and although indusium shape is homoplastic it does contain useful phylogenetic information that supports some of the larger clades recognised

Tree ferns: monophyletic groups and their relationships as revealed by four protein-coding plastid loci.

Tree ferns are a well-established clade within leptosporangiate ferns. Most of the 600 species (in seven families and 13 genera) are arborescent, but considerable morphological variability exists, spanning the giant scaly tree ferns (Cyatheaceae), the low, erect plants (Plagiogyriaceae), and the diminutive endemics of the Guayana Highlands (Hymenophyllopsidaceae). In this study, we investigate phylogenetic relationships within tree ferns based on analyses of four protein-coding, plastid loci (atpA, atpB, rbcL, and rps4). Our results reveal four well-supported clades, with genera of Dicksoniaceae (sensu ) interspersed among them: (A) (Loxomataceae, (Culcita, Plagiogyriaceae)), (B) (Calochlaena, (Dicksonia, Lophosoriaceae)), (C) Cibotium, and (D) Cyatheaceae, with Hymenophyllopsidaceae nested within. How these four groups are related to one other, to Thyrsopteris, or to Metaxyaceae is weakly supported. Our results show that Dicksoniaceae and Cyatheaceae, as currently recognised, are not monophyletic and new circumscriptions for these families are needed

Sleep Deprivation Detection for Real-Time Driver Monitoring using Deep Learning

International audienceWe propose a non-invasive method to detect sleep deprivation by evaluating a short video sequence of a subject. Computer Vision techniques are used to crop the face from every frame and classify it (within a Deep Learning framework) into two classes: " rested " or " sleep deprived ". The system has been trained on a database of subjects recorded under severe sleep deprivation conditions. A prototype has been implemented in a low-cost Android device proving its viability for real-time driver monitoring applications. Tests on real world data have been carried out and show encouraging performances but also reveal the need of larger datasets for training