Usage Bibliometrics

Scholarly usage data provides unique opportunities to address the known shortcomings of citation analysis. However, the collection, processing and analysis of usage data remains an area of active research. This article provides a review of the state-of-the-art in usage-based informetric, i.e. the use of usage data to study the scholarly process.Comment: Publisher's PDF (by permission). Publisher web site: books.infotoday.com/asist/arist44.shtm

Near-infrared H2 and continuum survey of extended green objects. II. Complete census for the northern Galactic plane

We discuss 94 Extended Green Objects (EGOs) in the northern Galactic plane cataloged by Cyganowski et al., based on near-infrared narrow H2 (2.122 μm) and continuum observations from the United Kingdom Infrared Telescope. This data set is three times larger than the one in our previous study and is unbiased by preselection. As discussed in the previous paper, the morphologies of the 4.5 μm emission generally resemble those of the near-infrared continuum, but are different from those of the H2 emission. Of our sample, only 28% of EGOs with H2 emission show similar morphologies between 4.5 μm and H2 emission. These results suggest that the 4.5 μm emission mainly comes from scattered continuum from the embedded young stellar objects, and partially from H2 emission. About half of EGOs are associated with H2 outflows, if the H 2 outflow incompleteness is considered. The H2 outflow detection rate for EGOs with K-band detections (61%) is significantly higher than for those without K-band detections (36%). This difference may be due to the fact that both H2 and K-band emissions are associated with outflows, i.e., H2 emission and K-band continuum are associated with shocks and outflow cavities, respectively. We also compared the correlation between the H2 outflows and Class I 44 GHz methanol masers from the literature. The methanol masers can be located upstream or downstream of the H2 outflows and some bright H2 spots or outflows are not associated with methanol masers, suggesting that methanol masers and H 2 emission trace different excitation conditions. © 2013. The American Astronomical Society. All rights reserved.

A 95 GHz Class I Methanol Maser Survey Toward A Sample of GLIMPSE Point Sources Associated with BGPS Clumps

We report a survey with the Purple Mountain Observatory (PMO) 13.7-m radio telescope for class I methanol masers from the 95 GHz (8_0 - 7_1 A^+) transition. The 214 target sources were selected by combining information from both the Spitzer GLIMPSE and 1.1 mm BGPS survey catalogs. The observed sources satisfy both the GLIMPSE mid-IR criteria of [3.6]-[4.5]>1.3, [3.6]-[5.8]>2.5, [3.6]-[8.0]>2.5 and 8.0 um magnitude less than 10, and also have an associated 1.1 mm BGPS source. Class I methanol maser emission was detected in 63 sources, corresponding to a detection rate of 29% for this survey. For the majority of detections (43), this is the first identification of a class I methanol maser associated with these sources. We show that the intensity of the class I methanol maser emission is not closely related to mid-IR intensity or the colors of the GLIMPSE point sources, however, it is closely correlated with properties (mass and beam-averaged column density) of the BGPS sources. Comparison of measures of star formation activity for the BGPS sources with and without class I methanol masers indicate that the sources with class I methanol masers usually have higher column density and larger flux density than those without them. Our results predict that the criteria log(S_{int})22.1, which utilizes both the integrated flux density (S_{int}) and beam-averaged column density (N_{H_{2}}^{beam}) of the BGPS sources, are very efficient for selecting sources likely to have an associated class I methanol maser. Our expectation is that searches using these criteria will detect 90% of the predicted number of class I methanol masers from the full BGPS catalog (~ 1000), and do so with a high detection efficiency (~75%).Comment: Accepted for publication in ApJ Supplement. 58 pages, 12 figures, 7 table

Lack of phenotypic and evolutionary cross-resistance against parasitoids and pathogens in Drosophila melanogaster

BackgroundWhen organisms are attacked by multiple natural enemies, the evolution of a resistance mechanism to one natural enemy will be influenced by the degree of cross-resistance to another natural enemy. Cross-resistance can be positive, when a resistance mechanism against one natural enemy also offers resistance to another; or negative, in the form of a trade-off, when an increase in resistance against one natural enemy results in a decrease in resistance against another. Using Drosophila melanogaster, an important model system for the evolution of invertebrate immunity, we test for the existence of cross-resistance against parasites and pathogens, at both a phenotypic and evolutionary level.MethodsWe used a field strain of D. melanogaster to test whether surviving parasitism by the parasitoid Asobara tabida has an effect on the resistance against Beauveria bassiana, an entomopathogenic fungus; and whether infection with the microsporidian Tubulinosema kingi has an effect on the resistance against A. tabida. We used lines selected for increased resistance to A. tabida to test whether increased parasitoid resistance has an effect on resistance against B. bassiana and T. kingi. We used lines selected for increased tolerance against B. bassiana to test whether increased fungal resistance has an effect on resistance against A. tabida.Results/ConclusionsWe found no positive cross-resistance or trade-offs in the resistance to parasites and pathogens. This is an important finding, given the use of D. melanogaster as a model system for the evolution of invertebrate immunity. The lack of any cross-resistance to parasites and pathogens, at both the phenotypic and the evolutionary level, suggests that evolution of resistance against one class of natural enemies is largely independent of evolution of resistance against the other

The CACTA transposon Bot1 played a major role in Brassica genome divergence and gene proliferation

We isolated and characterized a Brassica C genome-specific CACTA element, which was designated Bot1 (Brassica oleracea transposon 1). After analysing phylogenetic relationships, copy numbers and sequence similarity of Bot1 and Bot1 analogues in B. oleracea (C genome) versus Brassica rapa (A genome), we concluded that Bot1 has encountered several rounds of amplification in the oleracea genome only, and has played a major role in the recent rapa and oleracea genome divergence. We performed in silico analyses of the genomic organization and internal structure of Bot1, and established which segment of Bot1 is C-genome specific. Our work reports a fully characterized Brassica repetitive sequence that can distinguish the Brassica A and C chromosomes in the allotetraploid Brassica napus, by fluorescent in situ hybridization. We demonstrated that Bot1 carries a host S locus-associated SLL3 gene copy. We speculate that Bot1 was involved in the proliferation of SLL3 around the Brassica genome. The present study reinforces the assumption that transposons are a major driver of genome and gene evolution in higher plants

High-Resolution Single Nucleotide Polymorphism Analysis Distinguishes Recrudescence and Reinfection in Recurrent Invasive Nontyphoidal Salmonella Typhimurium Disease

Invasive nontyphoidal Salmonella Typhimurium disease is a common and frequently recurrent cause of bacteremia across sub-Saharan Africa. We use high-resolution single nucleotide polymorphism analysis to distinguish between reinfection and recrudescence in disease recurrence within single individuals over time

mGenomeSubtractor: a web-based tool for parallel in silico subtractive hybridization analysis of multiple bacterial genomes

mGenomeSubtractor performs an mpiBLAST-based comparison of reference bacterial genomes against multiple user-selected genomes for investigation of strain variable accessory regions. With parallel computing architecture, mGenomeSubtractor is able to run rapid BLAST searches of the segmented reference genome against multiple subject genomes at the DNA or amino acid level within a minute. In addition to comparison of protein coding sequences, the highly flexible sliding window-based genome fragmentation approach offered can be used to identify short unique sequences within or between genes. mGenomeSubtractor provides powerful schematic outputs for exploration of identified core and accessory regions, including searches against databases of mobile genetic elements, virulence factors or bacterial essential genes, examination of G+C content and binucleotide distribution bias, and integrated primer design tools. mGenomeSubtractor also allows for the ready definition of species-specific gene pools based on available genomes. Pan-genomic arrays can be easily developed using the efficient oligonucleotide design tool. This simple high-throughput in silico ‘subtractive hybridization’ analytical tool will support the rapidly escalating number of comparative bacterial genomics studies aimed at defining genomic biomarkers of evolutionary lineage, phenotype, pathotype, environmental adaptation and/or disease-association of diverse bacterial species. mGenomeSubtractor is freely available to all users without any login requirement at: http://bioinfo-mml.sjtu.edu.cn/mGS/