1,721,031 research outputs found
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe 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
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Teskearchaeota, a unique archaea group from hydrothermally impacted sediments from Guaymas Basin
Get PDFThis dissertation explores the phylogenetic position and metabolic capabilities of Teskearchaeota, a new phylum of archaea discovered in sediment cores collected from the Guaymas Basin, a young and active seafloor-spreading center in the Gulf of California, Mexico. Through the analysis of metagenome-assembled genomes (MAGs), we confirm that Teskearchaeota is phylogenetically distinct from any known archaeal phylum and falls within the TACK superphylum. The initial metabolic analysis suggests that Teskearchaeota is likely to be anaerobic and capable of using hydrogen as an energy source. The predicted genomes also indicate that these organisms oxidize small carbon molecules via fermentation. Further metabolic analysis will provide insights into the survival strategies of these organisms in the extreme conditions of deep-sea hydrothermal vents. This discovery expands our understanding of the diversity within the TACK superphylum and contributes to our knowledge of the evolution and role of microorganisms in extreme environments.Integrative Biolog
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Report on estimating prokaryotic recombination landscapes from genomic data
Get PDFRecombination plays a crucial role in the evolution of prokaryotic life. As genomic sequencing data become more widely available, many methods to estimate the rate of recombination have been developed to meet the increasingly high computation demand. Methods for estimating recombination rely on a number of signals resulting from recombination, including differentiation in linkage, phylogeny, and substitution rate. Here, I discuss different signals used to detect recombination, how they are incorporated into current recombination estimation software, and the potential limitations of that software or algorithm. I also discuss which of these methods can be applied to different types of sequencing data. Finally, I provide a detailed description of four commonly used programs for estimating recombination from genomic data in prokaryotes.Ecology, Evolution and Behavio
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Expansion of Armatimonadetes through marine sediment sequencing reveals three classes with unique ecological roles
Get PDFMarine sediments comprise one of the largest environments on the planet, and their microbial inhabitants are significant players in global carbon and nutrient cycles. With the advent of improved sampling techniques, recent scientific studies have shown the complexity of these communities and identified novel microorganisms from the ocean floor. Here we add to our understanding of understudied microbes by obtaining 77 metagenome-assembled genomes from the bacterial phylum Armatimonadetes in the Guaymas Basin, Gulf of California, and the Bohai Sea, coastal China. Seven of these MAGs are not classified at the class level. Thus, we propose to name these organisms Zipacnadia. Searches of public databases revealed that the 77 Armatimonadetes described in this study (including Zipacnadia) are globally distributed in hypoxic and anoxic environments and are dominant members of deep-sea sediments (up to 1.95% of the GB metagenomic raw reads). The Armatimonadetes described here also have unique metabolic capabilities for this phylum. They have pathways to reduce CO₂ to acetate via the Wood-Ljungdahl pathway (WLP) and generate energy through the oxidative branch of the Embden-Meyerhof-Parnas pathway using CO2 as an electron sink, maintaining the redox balance via WLP. Some of these organisms may also have an autotrophic lifestyle not previously identified in Armatimonadetes. Furthermore, these Armatimonadetes may play a role in sulfur and nitrogen cycling, using the intermediate compounds hydroxylamine and sulfite. The description of the Armatimonadetes identified in this study enhances our understanding of the diversity and metabolic potential of anoxic habitats worldwide.Marine Scienc
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Expansion of Deltaproteobacteria diversity from marine sediment reveals unique metabolic features
Get PDFDeltaproteobacteria are a ubiquitous class of bacteria that play a substantial role in carbon and nutrient cycling. However, our understanding of Deltaproteobacteria is biased towards cultured exemplars. To better understand the biodiversity and ecology of the Deltaproteobacteria, we obtained hundreds of unique, uncultured metagenome-assembled genomes (MAGs) from a variety of coastal and deep-sea sediments. These 402 Deltaproteobacteria MAGs represent a 28% increase in Deltaproteobacteria genomes. Phylogenomic analyses revealed 12 novel lineages which consist entirely of uncultured representatives. Among these are two lineages that appear to represent a new order, which are capable of denitrification and dissimilatory nitrate reduction to ammonia (DNRA). Metabolic inference of Deltaproteobacteria MAGs reveals extensive versatility, central carbon metabolism, and a broad distribution of the Wood-Ljungdahl pathway for CO2 fixation. 54% of Deltaproteobacteria MAGs encode dissimilatory sulfite reductases (DsrAB), and for those with the ability to reduce sulfate, several dsr genes are related to those from thermophiles. This study expands the genetic catalog of Deltaproteobacteria and provides a better ecological context for Deltaproteobacteria worldwide. The description of these new lineages highlights that there is much to be learned about this globally distributed proteobacteriaMarine Scienc
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe 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
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