1,721,151 research outputs found
Oomycete diversity determined via metabarcoding in two embayments in the Orkney Islands, Scotland, UK in 2016
No full textWater sampling was carried out weekly between April and October 2016. Water samples were taken from two shallow sites (less than 5 km apart) in the Orkneys. Sampling was done using a bucket at both sampling locations. Water for filtration was transported to the Orkney Lobster Hatchery where 500–1000 mL of water was filtered over 0.4 µm polycarbonate (PC) filter (Whatman, 47mm). Filters were stored at -20 °C until DNA isolation in the laboratory. The samples were processed at the AWI to produce a metabarcoding data set with the goal of analysing the general diversity at the two sites but also to investigate the dynamics of harmful algal bloom species (HABs). As the data also contained a wealth of information on protistan parasites they were used to produce an additional manuscript on oomycete infections in the planktonic foodweb at the two sites.
The bioinformatic processing of the raw sequence files was conducted as follows. The low-quality 3'-ends of the reads were trimmed by Trimmomatic (version 0.38) and the paired-ends were merged by VSEARCH (version 2.3.0). Cutadapt (version 1.19, was used to adjust the sequence orientation and to remove the forward and reverse primer matching sequence segments. Sequences were only kept in the sequence pool if both primer matching segments could be detected. To ensure a high sequence quality the remaining sequences were filtered by VSEARCH and only kept if the expected base error (sum of all base error probabilities) of a sequence was above 0.25. Chimeric sequences were predicted sample-wise by VSEARCH in de novo mode with default settings and removed from the sequence pool as well. Only samples which consisted of at least 10000 sequences after filtering were considered for further analyses. The remaining sequences were clustered into OTUs by the tool swarm (version 2.2.2) with default settings. For each OTU the most abundant amplicon was selected as representative and taxonomically annotated with the default classifier implemented in mothur (version 1.38.1). As reference the Protist Ribosomal Reference database (PR2), version 4.10 was chosen and the minimum confidence cut-off for annotation was set to a value of 80. Further details of the pipeline are provided in (Sprong, et al. 2020; doi:10.1016/j.seares.2020.101914)
Long-term changes in the seasonality of selected diatoms related to grazers and environmental conditions
No full textThe decoupling of trophic interactions could be one of the severe consequences of climate warming in aquatic systems. The timing of phytoplankton blooms, in particular, can affect competition within the plankton community as well as food-web interactions with zooplankton and fish. Using long-term data from Helgoland Roads in the southern North Sea, we examine diatom seasonality, using three representative diatom species combined with environmental and copepod time series over the last four decades. The long-term annual abundances of Guinardia delicatula, Thalassionema nitzschioides and Odontella aurita exhibited interannual variations and dissimilar cyclic patterns during the time period under study (1962–2008). Of the three diatoms, G. delicatula showed a significant trend towards earlier bloom timings for 1962–2008 and a later decline of its abundance over time was found. Grazing and water transparency explained most of the bloom timing fluctuations of the diatoms considered. The annual timing of occurrences of each diatom species was correlated with their preceding concentrations. Earlier bloom timings occurred when autumn/winter concentrations were higher than average and later bloom timings occurred when autumn/winter concentrations were lower than average. Different environmental and predation variables related to the diatom bloom timings were found suggesting that climate warming might not affect the onset of the blooms of the three diatom species in the same manner. The results of the multiple linear regression analyses showed that the timings of decline of the three diatoms were mainly correlated with decreasing nutrient concentrations. Sunshine duration could prolong the duration of the blooms of T. nitzschioides and O. aurita provided that enough nutrients were available. In the case of G. delicatula, however, sunshine duration was negatively correlated with its end of the growth period. G. delicatula and T. nitzschioides showed later decreases in abundances under warmer spring and summer temperatures. Such species specific differences in the sensitivity to the forcing variables could lead to shifts in community structure and could ultimately have wider implications to the overall ecosystem health of the North Sea
Abundance of the main protist groups in a subset of microscopy samples from leg 3 of the MOSAiC campaign
No full textThe data sets originates from the weekly sampling events (MOSAiC time series) during the MOSAiC campaign. Water samples from the CTD/Rosette were taken and fixed in Hexamin- buffered Formalin. 50ml subsamples were counted using the Utermöhl method. Counts were carried out with a Zeiss inverted microscope. The data set comprises bulk parameters with cell abundances (as cells/l) for the most abundant protist groups. In addition cell numbers for the toxic pennate diatom are provided separatel
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
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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