1,721,008 research outputs found
shaylematsuda/Mcap_CD_growth: Symbiont growth trade-offs
No full text<p>Data and scripts for the "Symbiont-mediated tradeoffs between growth and heat tolerance are modulated by light and temperature in the coral <em>Montipora capitata</em>" manuscript.
Shayle Matsuda, Mariah Opalek, Raphael Ritson-Williams, Ruth Gates, Ross Cunning</p>
shaylematsuda/Symbiont_Choice: v1.0.2
No full textData and scripts for "Temperature mediated acquisition of rare heterologous symbionts promotes survival of coral larvae under ocean warming" by Shayle B Matsuda, Leela J Chakravarti, Ross Cunning, Ariana S Huffmyer, Craig E Nelson, Ruth D Gates, Madeleine JH van Oppe
Data for: Patterns of bleaching and recovery of Montipora capitata in Kāneʻohe Bay, Hawaiʻi, USA
No full text<p>This repository includes data and analysis scripts to accompany:</p>
<p>Patterns of bleaching and recovery of Montipora capitata in Kāneʻohe Bay, Hawaiʻi, USA</p>
<p>Authors: Ross Cunning, Raphael Ritson-Williams, Ruth D. Gates</p>
<p>Journal: <em>Marine Ecology Progress Series</em></p>
<p>Link: doi:10.3354/meps11733</p>
<p>Description:</p>
<p>This work analyzes bleaching and recovery dynamics of <em>Symbiodinium</em> in <em>Montipora capitata</em> corals following a thermal stress event in Kāneʻohe Bay, Oʻahu (Hawaiʻi, USA) in late 2014. Corals were tagged and resampled 6 times between October 2014 and May 2015, and extracted DNA from each sample was used to measure symbiont to host cell ratios for both clade C and clade D <em>Symbiodinium</em>.</p>
<p>Contents:</p>
<p>Scripts:</p>
<ul>
<li>
<p><strong>setup.R:</strong> R script that imports and quality controls qPCR data in preparation for analysis.</p>
</li>
<li>
<p><strong>analysis.R:</strong> R script for all data analyses and figures presented in the manuscript.</p>
</li>
<li>
<p><strong>suppmethods.R:</strong> R script for analyses presented in the Supplement (fluorescence normalization, copy number estimation, ITS2 analysis, environmental data analysis).</p>
</li>
<li>
<p><strong>ITS2_analysis.txt:</strong> Shell script for bioinformatic analysis of <em>Symbiodinium</em> ITS2 data.</p>
</li>
</ul>
<p>Data:</p>
<ul>
<li>
<p><strong>data/coast_n83.shp/:</strong> Hawaii coastline shapefile, originally downloaded from here</p>
</li>
<li>
<p><strong>data/bleachedpair.png:</strong> Photograph of a bleached and non-bleached pair of <em>M. capitata</em> colonies used in Figure 1 (photo credit: R. Ritson-Williams).</p>
</li>
<li>
<p><strong>data/qPCR/:</strong> Directory containing .csv files of symbiont and host quantification data exported directly from Applied Biosystems StepOnePlus Software qPCR platform.</p>
</li>
<li>
<p><strong>data/ITS2/:</strong> Directory containing ITS2 sequence data .fastq files (raw data) and OTU tables (final result of bioinformatic analysis). Note that intermediate/temporary data files in bioinformatic analysis are not included in the repository.</p>
</li>
<li>
<p><strong>data/supp/:</strong> Directory containing data for fluorescence normalization and gene copy number estimation, presented in the Supplement.</p>
</li>
<li><strong>data/temp_light/:</strong> Directory containing temperature and light data recorded during the study, originally downloaded from Zenodo.
<ul>
<li>Links to Zenodo data repositories:
<ul>
<li>Temperature data: doi:10.5281/zenodo.53226</li>
<li>Light data: doi:10.5281/zenodo.53227</li>
</ul>
</li>
</ul>
</li>
</ul>
<p>Output:</p>
<ul>
<li><strong>output/:</strong> Directory containing the figures and tables produced by the analysis scripts and presented in the manuscript and the Supplement.</li>
</ul>
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
steponeR: R package for importing qPCR data from StepOne™ Software
No full text<p>This package reads qPCR data exported from StepOne™ Software (Life Technologies Corp.) into R and optionally calculates either target ratios or target quantities based on a standard curve.</p>
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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