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We currently output HDF5 (easy with pyh5) and then generate an XDMF file for it (I wish there was a nice python wrapper for this, but PETSc has petscgenxdmf.py for now).

["3D Visualization"]
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The character states as written do not correspond to how they are figured in Fig. 62. The states in the figure are as they were used in the matrix: 227-0 should be "absent" and 227-1 should be "present". In any case, this does not influence the result, of course.

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Interesting stuff. What are your thoughts on the possibility that the effects of cocaine on honey bee behavior might reflect adaptations for self-medication? Other studies support possible self-medication in honey bees, e.g.: [Increased Resin Collection after...

["self-medication"]
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There is no documented overlap of Leptosuchus and Smilosuchus (early to mid-Norian) with any Machaeroprosopus species (mid- to late Norian). The NA Rhaetian phytosaur is Redondasaurus (possibly synonymous with Machaeroprosopus, but a different species than the...

["Biostratigraphy"]
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The patterns shown in this figure are really interesting. Results from a year-round study would be of interest as well.

["bird window collisions"]
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There doesn't seem to be a place to provide feedback so I made a note on the preprint concerning some updates to the OncoLnc database: https://peerj.com/preprints/1780/#feedback-626. That note reads as: Dr....

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Hello, in Camarinha-Silva et al. 2014, the mean number of sequences per sample was 7682 ± 484, totalling 1 459 615 usable paired-end sequence reads. In your study, after quality filtering, a total of 782,683 paired-end reads, with an average of 41,194 reads per...

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In your conclusion for the optimized steps, number 7 recomends assigning taxonomy with BLAST. Did you test other approaches to taxonomy assignment? example: Wang Q, Garrity GM, Tiedje JM, Cole JR (2007). Naive Bayesian classifier for rapid assignment of rRNA...

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It would be very interesting to compare also a frequency of the antisocial punishment between these two localities. The Player 3 should be given also an opportunity to punish also the Player 1 who did not steal from the player 1. Our results suggest that the frequency...

["altruism victims"]
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This is a nice article. Did the authors observe brown rot of damaged fruits? Brown rot of apple fruits typically requires wounding (insect or bird) and I would imagine that damage caused by birds earlier in the fruit ripening phase would promote a larger fruit...

["plant disease"]
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Hello authors. A very interesting article. I would like to known what is the average size of the alginate beads used in this studies, and whether the effects observed could be related to the fact that some chemical signals such as TGF could have difficulties...

["tissue engineering","3D culture","cell differentiation"]
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Dear Kromann, your paper is an interesting read and covers an important topic! Like many computational methods, benchmarking is hard due to lack of high quality experimental data. I may have overlooked it (I hope not), but I did not find a section about the reference...

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The reason I ask is that standard laser printers (e. g. HP4000) that are used to make labels for pinned specimens are not satisfactory for alcohol-preserved material, because the letters float off the paper and become alphabet soup. I believe there is an Epson...

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You criticize my vouchering system by pointing out that "appendages glued to a card can only be viewed from a single perspective (i.e., only one wing surface can be examined)." If you examine the image at http://www.butterfliesofamerica.com/L/heliconius_tristero_types.htm...

["DNA voucher specimens"]
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I found myself reading Student's original paper on the t-test, and found on page 14 the following observations (quote transcription and emphasis both by me): %% Another thing which interferes with the comparison is the...