305,210 research outputs found
SILVA_123 Eukaryota taxonomic training data formatted for DADA2; plus version with (uncurrated) additional sequences
No full text<p>This is the Silva123 taxonomy reformatted to work with eukaryote sequences for dada2:</p>
<p><a href="https://zenodo.org/api/files/4f873b5b-fe02-4344-8c8b-c723c3caba67/SILVA_123_dada2.fasta">SILVA_123_dada2.fasta </a></p>
<p>It has been created using a script available <a href="https://github.com/derele/AA_Hyena/blob/master/R/convert_silva_taxonomy.r">here</a>.</p>
<p>To increase coverage (Silva has a low coverage for eukaryotes). Uncurrated additional sequences similar to ASVs found in the intestine of hyenas (BLAST) have been added. The script used for taxonomic annotation of these sequences is available <a href="https://github.com/derele/AA_Hyena/blob/master/scripts/blast2alltax_outfmt11.pl">here</a>. The file containing these additional (uncurrated!) sequences is:</p>
<p><a href="https://zenodo.org/api/files/4f873b5b-fe02-4344-8c8b-c723c3caba67/SILVA_123_dada2_exp.fasta?versionId=78a7526a-72e0-4707-ab5c-297671b5ff13">SILVA_123_dada2_exp.fasta </a></p>
<p>This expanded file has been used for taxonomic annotation in: </p>
<p><a href="https://doi.org/10.3389/fcimb.2017.00262">Heitlinger, E., Ferreira, S., Thierer, D., Hofer, H., & East, M. L. (2017). The intestinal eukaryotic and bacterial biome of spotted hyenas: the impact of social status and age on diversity and composition. <em>Frontiers in cellular and infection microbiology</em>, <em>7</em>, 262.</a></p>This is the version used in:
Emanuel Heitlinger, Susana C. M. Ferreira, Dagmar Thierer, Heribert Hofer, and Marion L. East (2017) The Intestinal Eukaryotic and Bacterial Biome of Spotted Hyenas: The Impact of Social Status and Age on Diversity and Composition Front. Cell. Infect. Microbio; 7: 262. doi: 10.3389/fcimb.2017.0026
Going Beyond Counting First Authors in Author Co-citation Analysis
No full textThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Dispelling the Myths Behind First-author Citation Counts
No full textWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
Author, publisher and bookseller : a tripartite synergy in Nigerian book industry
No full textThis work is about the roles of Author, Publisher and Bookseller in Book development in
Nigeria. The paper started by delving into the history of Book Publishing in Nigeria after
which it proceeded by defining who an author, a publisher, and a bookseller is and
expatiated on the indispensable roles of these key actors in Nigerian Book Industry and in
the emerging Information Society. Furthermore, the various constraints to book
development were identified while the paper advised on how the Book Industry can be
further promoted in Nigeria. However, the paper concluded and made recommendations
on how the Book sector can help in enhancing scholarship in the country
The transcriptome of the invasive eel swimbladder nematode parasite Anguillicola crassus
No full textABSTRACT: BACKGROUND: Anguillicola crassus is an economically and ecologically important parasitic nematode of eels. The native range of A. crassus is in East Asia, where it infects Anguilla japonica, the Japanese eel. A. crassus was introduced into European eels, Anguilla anguilla, 30 years ago. The parasite is more pathogenic in its new host than in its native one, and is thought to threaten the endangered An. anguilla across its range. The molecular bases for the increased pathogenicity of the nematodes in their new hosts is not known. RESULTS: A reference transcriptome was assembled for A. crassus from Roche 454 pyrosequencing data. Raw reads (756,363 total) from nematodes from An. japonica and An. anguilla hosts were filtered for likely host contaminats and ribosomal RNAs. The remaining 353,055 reads were assembled into 11,372 contigs of a high confidence assembly (spanning 6.6 Mb) and an additional 21,153 singletons and contigs of a lower confidence assembly (spanning an additional 6.2 Mb). Roughly 55% of the high condence assembly contigs were annotated with domain- or protein sequence similarity derived functional information. Sequences conserved only in nematodes, or unique to A. crassus were more likely to have secretory signal peptides. Thousands of high quality single nucleotide polymorphisms were identified, and coding polymorphism was correlated with diffrential expression between individual nematodes. Transcripts identfied as being under positive selection were enriched in peptidases. Enzymes involved in energy metabolism were enriched in the set of genes differentially expressed between European and Asian A. crassus. CONCLUSIONS: The reference transcriptome of A. crassus is of high quality, and will serve as a basis for future work on the invasion biology of this important parasite. The polymorphisms identied will provide a key tool set for analysis of population structure and identication of genes likely to be involved in increased pathogenicity in European eel hosts. The identication of peptidases under positive selection is a first step in this programme
The role of the head and tail domain in lamin structure and assembly : analysis of bacterially expressed chicken lamin A and truncated B2 lamins
No full textNuclear lamins like cytoplasmic intermediate filament proteins exhibit a characteristic tripartite domain structure with a segmented alpha-helical rod domain flanked by an N-terminal head and a C-terminal tail domain. To examine the influence of the head and tail domains on the structure and assembly properties of nuclear lamins, we have engineered "headless," "tailless," and "rod" chicken lamin B2 cDNAs and expressed them in Escherichia coli. A full-length chicken lamin A cDNA was also expressed in E. coli, and the recombinant protein compared with the structure and assembly properties of full-length chicken lamin B2 (E. Heitlinger et al. (1991) J. Cell Biol. 113, 485-495). As with lamin B2, at their first level of structural organization, lamin A and the headless lamin B2 formed myosin-like dimers consisting of a 51- to 52-nm-long tail flanked by two globular heads at one end. Similarly, the tailless and rod lamin B2 fragments formed tropomyosin-like dimers consisting of a 51 to 52-nm-long rod. In contrast to the lateral mode of association of cytoplasmic IF dimers into four-chain tetramers, at their second level of structural organization, lamin A dimers, just as lamin B2 dimers (E. Heitlinger et al. (1991) J. Cell Biol. 113, 485-495), associated longitudinally to form polar head-to-tail polymers. Whereas dimers made of the truncated B2 headless and rod lamins had lost their propensity to associate head-to-tail, tailless lamin B2 dimers revealed an enhanced head-to-tail association. Finally, at their third level of structural organization, rather than assembling into stable 10-nm filaments, both lamin A and the three truncated B2 lamins formed paracrystalline arrays exhibiting distinct transverse banding patterns with axial repeats of either 24 or 48-49 nm depending on the species
[Report to Chief J. E. Curry, by an unknown author #2]
No full textReport to Chief J. E. Curry, by an unknown author. The report contains a list of officers who gave depositions to the United States Attorney
[Report to Chief J. E. Curry, by an unknown author #1]
No full textReport to Chief J. E. Curry, by an unknown author. The report contains a list of officers who gave depositions to the United States Attorney
Mining e-mail content for author identification forensics
No full textWe describe an investigation into e-mail content mining for author identification, or authorship attribution, for the purpose of forensic investigation. We focus our discussion on the ability to discriminate between authors for the case of both aggregated e-mail topics as well as across different email topics. An extended set of e-mail document features including structural characteristics and linguistic patterns were derived and, together with a Support Vector Machine learning algorithm, were used for mining the e-mail content. Experiments using a number of e-mail documents generated by different authors on a set of topics gave promising results for both aggregated and multi-topic author categorisation
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