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Dear Authors, Thanks for providing and explaining these important principles. Regarding the "reasons that a commit reference together with a repository URL is not recommended for the purposes of software citation" I wonder about your opinions on the following...

["GitLab","GitHub","software citation"]
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I am agree with your interpretation. In the story telling of the Thecosomata diversyfying, I did not clearly mentionned the ecological replacment theory of ammonnites by (at least) the thecosomata, it was out of scope our article. However it was clearly what I...

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It's not clear what the terms in the equation denote. Am I correct to establish from the Calculations spreadsheet and Burgers & Chiappe (1999) that: Cl is the lift coefficient (taken as 1) f the flapping frequency Amp the amplitude of a flap U...

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The UT Knoxville Libraries, where I am employed as a librarian (https://libguides.utk.edu/veterinaryinformation) subscribe to the Web of Science Core Collection database. We also provide access to other databases relevant to this review on the Web of Science...

["methodology","literature reviews","systematic reviews","librarians","search strategies","databases","database selection"]
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We had overlooked Stevens et al. 2014 in which the same 12S primers were used to successfully amplify opossum DNA. http://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0003047 Stevens, L., Monroy, M. C., Rodas, A. G., & Dorn, P. L. (2014). Hunting,...

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"The default assumption should be that methodological weaknesses are due to ignorance rather than bad faith" (lines 138-139). Why does this assumption not extend to the discussion of literature reviews in the next paragraph? Why would selective or inaccurate reporting...

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First, I want to say that I am glad to see a paper on this paradoxical reef. We have some similar data for this area (for a different question) and we have a many sites along Barú island. It would be interesting to use your results as a comparison but the data...

["Coral cover data"]
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What's the exact meaning of the 'personal attention'?

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There are no black circles on the current version of the figure

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Dear authors ! What is the software to open your raw data CSV file with ? Microsoft Excel does not work properly Thank you!

["Raw data"]
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I noticed that only one source was searched, Google Scholar (section 2.1 of the preprint). For a systematic review, Google Scholar is problematic, especially if it is the only source searched. See https://www.ncbi.nlm.nih.gov/pubmed/27076802. I wonder if...

["methodology","literature reviews","systematic reviews","librarians","Cochrane","search strategies","databases","database selection"]
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Has anyone sampled the hindgut contents (possibly at different stages of fermentation) to determine what proportion of secondary metabolites remain in comparison to the concentrations in the ingested foliage? This seems like a key point to determine to what extent...

["microbiota","plant secondary metabolites","volatile organic compounds","xenobiotics"]
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Have you work just on literature compiling all the dinosaur bone findings from BC or have you seen the specimens in the museum where they are housed?

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In your study VSH factor counting was done by dividing the number of cells opened by bees with the number of cells examined. This was done by comparing fotographs taken at 10 days versus 20 days brood age. The porpotion of opened cells together with infestation...

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Was figure 2 directly generated using MEME or another package?

["motifs","software"]

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