Host Plant Suitability and a Test of the Feeding Specialization Hypothesis Using \u3ci\u3ePapilio Cresphontes\u3c/i\u3e (Lepidoptera: Papilionidae)

The concept that host plant favorites would be used for more rapid and/or efficient growth of the locally adapted individuals was tested in a preliminary way using the giant swallowtail butterfly, Papilio cresphontes. Populations feeding only on northern prickly ash, Zanthoxylum americanum (from Wisconsin), primarily (or exclusively) on hoptree, Ptelea trifoliata (in Ohio) and on lime prickly ash, Z. fagara, or Citrus, (in Florida) were compared on alternate hosts and on their actual local hosts under controlled environmental conditions. While the results with final instar larvae generally support the feeding specialization hypothesis with regard to more rapid and/or more efficient growth on local food plant favorites, we are hesitant to extrapolate these results to the species as a whole for several reasons dis- cussed herein

Mark-Release-Recapture Experiments on the Effectiveness of Methyl Eugenol–Spinosad Male Annihilation Technique Against an Invading Population of Bactrocera dorsalis

Bactrocera dorsalis is a pest of major concern in fruit-growing areas where it is not established. Control and eradication often employs male annihila- tion technique, using methyl eugenol as an attractant (MAT-ME). We conduced a small-scale mark-release-recapture study comparing two densities of MAT-ME (“high” = 225 spots per km2; “low” = 100 spots per km2) with a control by counting males recaptured in sentinel traps baited with ME 40 m from the release point. We hypothesized that recaptures would be reduced under the two MAT treatments by equivalent amounts compared with the control, reflecting male mortality from the treatments. We found a large degree of variation in trap recaptures between replicates and treatments, and no significant difference between recaptures under the high treatment and control. Recaptures were significantly lower under the low treatment, indicating greater mortality compared with control and high. We propose the “MAT-ME saturation hypothesis” to explain this result: increasing the number of stations per square mile increases mortality of receptive males until too many stations create a high enough background of ME that the males don’t effectively follow a gradient to MAT sources. Our findings highlight that further research into the effect of increasing MAT-ME spot density on male mortality is needed

A framework for mapping, visualisation and automatic model creation of signal-transduction networks

An intuitive formalism for reconstructing cellular networks from empirical data is presented, and used to build a comprehensive yeast MAP kinase network. The accompanying rxncon software tool can convert networks to a range of standard graphical formats and mathematical models

Experimental active control of a typical section using a trailing-edge flap

This paper presents an experimental implementation of an active control system used to suppress flutter in a typical section airfoil. The H2 optimal control system design is based on experimental system identifications of the transfer functions between three measured system variables - pitch, plunge, and flap position - and a single control signal that commands the flap of the airfoil. Closed-loop response of the airfoil demonstrated gust alleviation below the open-loop flutter boundary. In addition, the flutter boundary was extended by 12.4% through the application of active control. Cursory robustness tests demonstrate stable control for variations in flow speed of ± 10%

Heliogyro Solar Sail Research at NASA

The recent successful flight of the JAXA IKAROS solar sail has renewed interest within NASA in spinning solar sail concepts for high-performance solar sailing. The heliogyro solar sail, in particular, is being re-examined as a potential game-changing architecture for future solar sailing missions. In this paper, we present an overview of ongoing heliogyro technology development and feasibility assessment activities within NASA. In particular, a small-scale heliogyro solar sail technology demonstration concept will be described. We will also discuss ongoing analytical and experimental heliogyro structural dynamics and controls investigations and provide an outline of future heliogyro development work directed toward enabling a low cost heliogyro technology demonstration mission ca. 2020

Evolutionary Modeling and Prediction of Non-Coding RNAs in Drosophila

We performed benchmarks of phylogenetic grammar-based ncRNA gene prediction, experimenting with eight different models of structural evolution and two different programs for genome alignment. We evaluated our models using alignments of twelve Drosophila genomes. We find that ncRNA prediction performance can vary greatly between different gene predictors and subfamilies of ncRNA gene. Our estimates for false positive rates are based on simulations which preserve local islands of conservation; using these simulations, we predict a higher rate of false positives than previous computational ncRNA screens have reported. Using one of the tested prediction grammars, we provide an updated set of ncRNA predictions for D. melanogaster and compare them to previously-published predictions and experimental data. Many of our predictions show correlations with protein-coding genes. We found significant depletion of intergenic predictions near the 3′ end of coding regions and furthermore depletion of predictions in the first intron of protein-coding genes. Some of our predictions are colocated with larger putative unannotated genes: for example, 17 of our predictions showing homology to the RFAM family snoR28 appear in a tandem array on the X chromosome; the 4.5 Kbp spanned by the predicted tandem array is contained within a FlyBase-annotated cDNA

The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text

BACKGROUND: Determining usefulness of biomedical text mining systems requires realistic task definition and data selection criteria without artificial constraints, measuring performance aspects that go beyond traditional metrics. The BioCreative III Protein-Protein Interaction (PPI) tasks were motivated by such considerations, trying to address aspects including how the end user would oversee the generated output, for instance by providing ranked results, textual evidence for human interpretation or measuring time savings by using automated systems. Detecting articles describing complex biological events like PPIs was addressed in the Article Classification Task (ACT), where participants were asked to implement tools for detecting PPI-describing abstracts. Therefore the BCIII-ACT corpus was provided, which includes a training, development and test set of over 12,000 PPI relevant and non-relevant PubMed abstracts labeled manually by domain experts and recording also the human classification times. The Interaction Method Task (IMT) went beyond abstracts and required mining for associations between more than 3,500 full text articles and interaction detection method ontology concepts that had been applied to detect the PPIs reported in them.RESULTS:A total of 11 teams participated in at least one of the two PPI tasks (10 in ACT and 8 in the IMT) and a total of 62 persons were involved either as participants or in preparing data sets/evaluating these tasks. Per task, each team was allowed to submit five runs offline and another five online via the BioCreative Meta-Server. From the 52 runs submitted for the ACT, the highest Matthew's Correlation Coefficient (MCC) score measured was 0.55 at an accuracy of 89 and the best AUC iP/R was 68. Most ACT teams explored machine learning methods, some of them also used lexical resources like MeSH terms, PSI-MI concepts or particular lists of verbs and nouns, some integrated NER approaches. For the IMT, a total of 42 runs were evaluated by comparing systems against manually generated annotations done by curators from the BioGRID and MINT databases. The highest AUC iP/R achieved by any run was 53, the best MCC score 0.55. In case of competitive systems with an acceptable recall (above 35) the macro-averaged precision ranged between 50 and 80, with a maximum F-Score of 55. CONCLUSIONS: The results of the ACT task of BioCreative III indicate that classification of large unbalanced article collections reflecting the real class imbalance is still challenging. Nevertheless, text-mining tools that report ranked lists of relevant articles for manual selection can potentially reduce the time needed to identify half of the relevant articles to less than 1/4 of the time when compared to unranked results. Detecting associations between full text articles and interaction detection method PSI-MI terms (IMT) is more difficult than might be anticipated. This is due to the variability of method term mentions, errors resulting from pre-processing of articles provided as PDF files, and the heterogeneity and different granularity of method term concepts encountered in the ontology. However, combining the sophisticated techniques developed by the participants with supporting evidence strings derived from the articles for human interpretation could result in practical modules for biological annotation workflows

A communal catalogue reveals Earth's multiscale microbial diversity

Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.Peer reviewe

A communal catalogue reveals Earth’s multiscale microbial diversity

Our growing awareness of the microbial world’s importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial diversity