cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.801077.v3
title: Aboobaker Lab Schmidtea mediterranea transcriptome dataset

description: This fileset contains data associated with the consolidated Schmidtea mediterranea transcriptome. The publication associated with this fileset is currently under review. This transcriptome was consolidated using 5 independently assembled transcriptomes: -Blythe MJ, Kao D, Malla S, Rowsell J, Wilson R, et al. (2010) A Dual Platform Approach to Transcript Discovery for the Planarian Schmidtea Mediterranea to Establish RNAseq for Stem Cell and Regeneration Biology. PLoS ONE 5(12): e15617. doi:10.1371/journal.pone.0015617 -Catherine Adamidi, Yongbo Wang, Dominic Gruen, et al. (2011) De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics. Genome Research 2011. doi:10.1101/gr.113779.110 -Thomas Sandmann, Matthias C Vogg, Suthira Owlarn, et al. (2011) The head-regeneration transcriptome of the planarian Schmidtea mediterranea. Genome Biology 2011, 12:R76 doi:10.1186/gb-2011-12-8-r76 -Resch AM, Palakodeti D, Lu Y-C, Horowitz M, Graveley BR (2012) Transcriptome Analysis Reveals Strain-Specific and Conserved Stemness Genes in Schmidtea mediterranea. PLoS ONE 7(4): e34447. doi:10.1371/journal.pone.0034447 -Labbé, R. M., Irimia, M., Currie, K. W., Lin, A., Zhu, S. J., Brown, D. D.R., Ross, E. J., Voisin, V., Bader, G. D., Blencowe, B. J. and Pearson, B. J. (2012), A Comparative Transcriptomic Analysis Reveals Conserved Features of Stem Cell Pluripotency in Planarians and Mammals. STEM CELLS, 30: 1734–1745. doi: 10.1002/stem.1144 The following files are included in this fileset: OX_smed_1.0.fa - transcriptome sequences in fasta format. OX_smed_1.0.blast - cleaned blast results for transcriptome. Hits to hypotheticals or unknowns are filtered out. OX_smed_1.0.go - Gene ontology results for transcriptome. OX_smed_1.0.pfam - PFAM HMM-A scan results for transcriptome. OX_smed_1.0.tf - Potential transcription factors found in the transcriptome using DBD transcription factor database. OX_smed_1.0.source - The source transcripts/EST that made up each consolidated transcript.
DOI: 10.6084/m9.figshare.801049.v1
title: miR-30 Data for Figures

description: Data File 1. Plasmid Sequences Figure 1 data. Cells were transfected with an miR-30ac2 expression plasmid (“G30ac2”) or a control plasmid (“Gscr”). RNA was isolated and qRT-PCR was performed to measure the indicated transcripts. Expression was quantified using the delta-delta method. Figure 2 data. Cells were transfected with the miR-30ac2 expression plasmid “pSLIKG-miR30ac2”) or a control plasmid (“pSLIKG-Scr”), plus the indicated luciferase reported plasmid. Renilla and firefly luciferase activities were measured in cell exctracts. The firefly luciferase activity was used to normalize for transfection efficiency, and further correction was performed to control for the effects of the reporter plasmids and the miRNA expression plasmid. Comparison was made for each reporter plasmid between the miR-30ac2 expression plasmid and the control plasmid, and averages, standard error, and p-values were calculated. Figure 3 data. Table of PITA and Targetscan scores (if available) for the indicated UTRs, with the corresponding luciferase expression data from Figure 2.
DOI: 10.6084/m9.figshare.801077.v4
title: Aboobaker Lab Schmidtea mediterranea transcriptome dataset

description: This fileset contains data associated with the consolidated Schmidtea mediterranea transcriptome. The publication associated with this fileset is currently under review. This transcriptome was consolidated using 5 independently assembled transcriptomes: -Blythe MJ, Kao D, Malla S, Rowsell J, Wilson R, et al. (2010) A Dual Platform Approach to Transcript Discovery for the Planarian Schmidtea Mediterranea to Establish RNAseq for Stem Cell and Regeneration Biology. PLoS ONE 5(12): e15617. doi:10.1371/journal.pone.0015617 -Catherine Adamidi, Yongbo Wang, Dominic Gruen, et al. (2011) De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics. Genome Research 2011. doi:10.1101/gr.113779.110 -Thomas Sandmann, Matthias C Vogg, Suthira Owlarn, et al. (2011) The head-regeneration transcriptome of the planarian Schmidtea mediterranea. Genome Biology 2011, 12:R76 doi:10.1186/gb-2011-12-8-r76 -Resch AM, Palakodeti D, Lu Y-C, Horowitz M, Graveley BR (2012) Transcriptome Analysis Reveals Strain-Specific and Conserved Stemness Genes in Schmidtea mediterranea. PLoS ONE 7(4): e34447. doi:10.1371/journal.pone.0034447 -Labbé, R. M., Irimia, M., Currie, K. W., Lin, A., Zhu, S. J., Brown, D. D.R., Ross, E. J., Voisin, V., Bader, G. D., Blencowe, B. J. and Pearson, B. J. (2012), A Comparative Transcriptomic Analysis Reveals Conserved Features of Stem Cell Pluripotency in Planarians and Mammals. STEM CELLS, 30: 1734–1745. doi: 10.1002/stem.1144 The following files are included in this fileset: OX_smed_1.0.fa - transcriptome sequences in fasta format. OX_smed_1.0.blast - cleaned blast results for transcriptome. Hits to hypotheticals or unknowns are filtered out. OX_smed_1.0.go - Gene ontology results for transcriptome. OX_smed_1.0.pfam - PFAM HMM-A scan results for transcriptome. OX_smed_1.0.tf - Potential transcription factors found in the transcriptome using DBD transcription factor database. OX_smed_1.0.source - The source transcripts/EST that made up each consolidated transcript. OX_Gtig_0.1.fa - G. tigrina transcriptome assembled from Roche 454 reads. Supp01-08 - Supplemental files for publication in submission.
DOI: 10.6084/m9.figshare.799813
title: Optimized calcium carbonate clusters at HF/6-31G* level of theory

description: These files contain the structures of the dimers, trimers, tetramers, pentamers, hexamers and heptamers of CaCO3 that we could identify as energy minima at the HF/6-31G* level of theory. Please cite the original paper http://www.springerlink.com/content/5q433p2575x12025/abstract/
DOI: 10.6084/m9.figshare.799823
title: Planck maps projected on a Truncated Icosahedron

description: Planck Temperature maps of the Microwave sky from 30 to 857 GHz (from the Planck 1st Data Release) projected on a Truncated icosahedron (i.e. soccer-ball-like).
DOI: 10.6084/m9.figshare.799813.v2
title: Optimized calcium carbonate clusters at HF/6-31G* level of theory

description: These files contain the structures of the dimers, trimers, tetramers, pentamers, hexamers and heptamers of CaCO3 that we could identify as energy minima at the HF/6-31G* level of theory. Please cite the original paper http://www.springerlink.com/content/5q433p2575x12025/abstract/
DOI: 10.6084/m9.figshare.799813.v1
title: Optimized calcium carbonate clusters at HF/6-31G* level of theoy

description: These files contain the structures of the dimers, trimers, tetramers, pentamers, hexamers and heptamers of CaCO3 that we could identify as energy minima at the HF/6-31G* level of theory. Please cite the original paper http://www.springerlink.com/content/5q433p2575x12025/abstract/
DOI: 10.6084/m9.figshare.799779
title: Calix[4]resorcinarene R8B1 (BR-) isotherm

description: Calix[4]resorcinarene surface pressure isotherm for the calix R8B1 (BR-). File contains the calculations for area per molecule and a diagram showing the exact structure of this calix molecule.
DOI: 10.6084/m9.figshare.799780
title: Calix[4]resorcinarene R8B2 (BR-) isotherm

description: Calix[4]resorcinarene surface pressure isotherm for the calix <strong>R8B2 (BR-)</strong>. File contains the calculations for area per molecule and a diagram showing the exact structure of this calix molecule.
DOI: 10.6084/m9.figshare.799781
title: Calix[4]resorcinarene surface pressure isotherms

description: This is a set of surface pressure isotherm data collected on 10 diffrent calix[4]resorcinarenes. Each isotherm was produced using a Nima alternate layer trough and a Nima wilhelmy plate system. Each isotherm was run at 50 cm/min. This data is from my thesis (see link)
DOI: 10.6084/m9.figshare.799778
title: Calix[4]resorcinarene R7B2 isotherm

description: Calix[4]resorcinarene surface pressure isotherm for the calix R7B2. File contains the calculations for area per molecule and a diagram showing the exact structure of this calix molecule.
DOI: 10.6084/m9.figshare.799780.v1
title: Calix[4]resorcinarene R8B2 (BR-) isotherm

description: Calix[4]resorcinarene surface pressure isotherm for the calix <strong>R8B2 (BR-)</strong>. File contains the calculations for area per molecule and a diagram showing the exact structure of this calix molecule.
DOI: 10.6084/m9.figshare.799777
title: Calix[4]resorcinarene R6B1 isotherm

description: Calix[4]resorcinarene surface pressure isotherm for the calix R6B1. File contains the calculations for area per molecule and a diagram showing the exact structure of this calix molecule.
DOI: 10.6084/m9.figshare.799778.v1
title: Calix[4]resorcinarene R7B2 isotherm

description: Calix[4]resorcinarene surface pressure isotherm for the calix R7B2. File contains the calculations for area per molecule and a diagram showing the exact structure of this calix molecule.
DOI: 10.6084/m9.figshare.799779.v1
title: Calix[4]resorcinarene R8B1 (BR-) isotherm

description: Calix[4]resorcinarene surface pressure isotherm for the calix R8B1 (BR-). File contains the calculations for area per molecule and a diagram showing the exact structure of this calix molecule.
DOI: 10.6084/m9.figshare.799781.v1
title: Calix[4]resorcinarene surface pressure isotherms

description: This is a set of surface pressure isotherm data collected on 10 diffrent calix[4]resorcinarenes. Each isotherm was produced using a Nima alternate layer trough and a Nima wilhelmy plate system. Each isotherm was run at 50 cm/min. This data is from my thesis (see link)
DOI: 10.6084/m9.figshare.799773
title: Calix[4]resorcinarene R4B1(NMeC16) isotherm

description: Calix[4]resorcinarene surface pressure isotherm for the calix R4B1(NMeC16). File contains the calculations for area per molecule and a diagram showing the exact structure of this calix molecule.
DOI: 10.6084/m9.figshare.799774
title: Calix[4]resorcinarene R4B1(NMeC18) isotherm

description: Calix[4]resorcinarene surface pressure isotherm for the calix R4B1(NMeC18). File contains the calculations for area per molecule and a diagram showing the exact structure of this calix molecule.
DOI: 10.6084/m9.figshare.799775
title: Calix[4]resorcinarene R4B2 (NMeC12) isotherm

description: Calix[4]resorcinarene surface pressure isotherm for the calix R4B2 (NMeC12). File contains the calculations for area per molecule and a diagram showing the exact structure of this calix molecule
DOI: 10.6084/m9.figshare.799776
title: Calix[4]resorcinarene R4B2 (NMeC16) isotherm

description: Calix[4]resorcinarene surface pressure isotherm for the calix R4B2 (NMeC16). File contains the calculations for area per molecule and a diagram showing the exact structure of this calix molecule.
DOI: 10.6084/m9.figshare.799777.v1
title: Calix[4]resorcinarene R6B1 isotherm

description: Calix[4]resorcinarene surface pressure isotherm for the calix R6B1. File contains the calculations for area per molecule and a diagram showing the exact structure of this calix molecule.
DOI: 10.6084/m9.figshare.799773.v1
title: Calix[4]resorcinarene R4B1(NMeC16) isotherm

description: Calix[4]resorcinarene surface pressure isotherm for the calix R4B1(NMeC16). File contains the calculations for area per molecule and a diagram showing the exact structure of this calix molecule.
DOI: 10.6084/m9.figshare.799774.v1
title: Calix[4]resorcinarene R4B1(NMeC18) isotherm

description: Calix[4]resorcinarene surface pressure isotherm for the calix R4B1(NMeC18). File contains the calculations for area per molecule and a diagram showing the exact structure of this calix molecule.
DOI: 10.6084/m9.figshare.799775.v1
title: Calix[4]resorcinarene R4B2 (NMeC12) isotherm

description: Calix[4]resorcinarene surface pressure isotherm for the calix R4B2 (NMeC12). File contains the calculations for area per molecule and a diagram showing the exact structure of this calix molecule
DOI: 10.6084/m9.figshare.799769
title: When you tweet upon a star

description: I have an ongoing search for tweets containing either the word astronomy or astrophysics, which lets me look at how often the tweet "According to Astronomy, when you wish upon a star, you're actually a few million years too late. That star is dead. Just like your dreams.", and variants, is repeated or retweeted. The graph, wish-upon-a-star-tweet-times.svg, shows the number of all tweets per day that contain either astronomy or astrophysics (red bars) and those that contain the phrase "According to Astronomy, when you wish upon a star" (blue bars). Unfortunately the search was not running for the whole period of the graph, which is why the count drops to near zero at times. The graph is missing a small number of tweets from before the start of July this year (the X axis is labelled year/month/day), just to keep the data readable. Of the 254729 tweets, 15668 are copies of this tweet; that is, 6 percent of Astronomy and Astrophysics tweets! Amazingly enough, more than half the tweets on Saturday, September 14th 2013 were about this. See the referenced articles, by my colleague Karen Masters and Phil 'Bad Astronomer' Plait, for more information on why this tweet is not scientifically accurate, and to see how long this has been floating around the internet. The tab-separated file tweet-upon-a-star-top20.tsv shows those tweets that were replied to the most during the search; this only uses the information provided by Twitter during the search, so can miss some links between tweets depending on how they were created or modified. It shows, amongst other things, that: 1 - many accounts are linked to the spread of this information 2 - the same account (handle in the table) repeats the same information at different times 3 - the third- and fourth-most repeated tweets are for a much-more interesting subject, that of Cecilia Payne-Gaposchkin's contributions to Astrophysics. Please note that, as with any Twitter study, the results here are incomplete since I have no guarantee that the search I am running returns all matching tweets. If the fraction of general astronomy and astrophysics tweets returned is different than that of the "wish upon a star" tweets then this would skew the results.
DOI: 10.6084/m9.figshare.799771
title: Calix[4]resorcinarene R3B5(NMeC18) isotherm

description: Calix[4]resorcinarene surface pressure isotherm for the calix RxBx. File contains the calculations for area per molecule and a diagram showing the exact structure of this calix molecule.
DOI: 10.6084/m9.figshare.799772
title: Calix[4]resorcinarene C11 isotherm

description: Calix[4]resorcinarene surface pressure isotherm for the calix C11. File contains the calculations for area per molecule and a diagram showing the exact structure of this calix molecule
DOI: 10.6084/m9.figshare.799776.v1
title: Calix[4]resorcinarene R4B2 (NMeC16) isotherm

description: Calix[4]resorcinarene surface pressure isotherm for the calix R4B2 (NMeC16). File contains the calculations for area per molecule and a diagram showing the exact structure of this calix molecule.
DOI: 10.6084/m9.figshare.799772.v1
title: Calix[4]resorcinarene C11 isotherm

description: Calix[4]resorcinarene surface pressure isotherm for the calix C11. File contains the calculations for area per molecule and a diagram showing the exact structure of this calix molecule
DOI: 10.6084/m9.figshare.799771.v1
title: Calix[4]resorcinarene R3B5(NMeC18) isotherm

description: Calix[4]resorcinarene surface pressure isotherm for the calix RxBx. File contains the calculations for area per molecule and a diagram showing the exact structure of this calix molecule.
DOI: 10.6084/m9.figshare.799759
title: Raw sequence reads for Chrysiogenes arsenatis

description: Raw sequencing reads (Illumina 84bp and Sanger ~1000bp) used in the draft genome assembly of Chrysiogenes arsenatis.
DOI: 10.6084/m9.figshare.799760
title: Psychosocial Health Problems Associated with Increased HIV Risk Behavior among Men Who Have Sex with men in Nepal: a cross-sectional survey

description: Study examined the association between MSM sub-populations, psychosocial health problems and support, access to prevention and non-use of condoms.
DOI: 10.6084/m9.figshare.799759.v1
title: Raw sequence reads for Chrysiogenes arsenatis

description: Raw sequencing reads (Illumina 84bp and Sanger ~1000bp) used in the draft genome assembly of Chrysiogenes arsenatis.
DOI: 10.6084/m9.figshare.799760.v1
title: Psychosocial Health Problems Associated with Increased HIV Risk Behavior among Men Who Have Sex with men in Nepal: a cross-sectional survey

description: Study examined the association between MSM sub-populations, psychosocial health problems and support, access to prevention and non-use of condoms.
DOI: 10.6084/m9.figshare.799743
title: Squence data for BACE evolution paper

description: A set of FASTA files from: A Tale of Two Drug Targets: The Evolutionary History of BACE1 and BACE2 Christopher Southan and John M Hancock Frontiers, submitted
DOI: 10.6084/m9.figshare.799716
title: Gaussian Job Archive for F4S2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.799718
title: WhichCyp SVM modelling data

description: output from R
DOI: 10.6084/m9.figshare.799743.v1
title: Squence data for BACE evolution paper

description: A set of FASTA files from: A Tale of Two Drug Targets: The Evolutionary History of BACE1 and BACE2 Christopher Southan and John M Hancock Frontiers, submitted
DOI: 10.6084/m9.figshare.799718.v1
title: WhichCyp SVM modelling data

description: output from R
DOI: 10.6084/m9.figshare.799711
title: Minicurso: Noções Básicas Sobre o R Aplicadas à Engenharia Florestal

description: R markdown code used in the preparation of the presentation at workshop section of academic week of forestry - CAV/UDESC Codigo de R markdown utilizado na preparação da apresentação realizada na seção de minicurso da semana academica em engenharia florestal - CAV/UDESC
DOI: 10.6084/m9.figshare.799714
title: Gaussian Job Archive for C33H27CuI2N3P

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.799716.v1
title: Gaussian Job Archive for F4S2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.799703
title: Binding energy of trypsin-BPTI complex with PyGBe and APBS

description: This file bundle includes data, figures and plotting scripts of solvation energy and binding energy calculations for trypsin-BPTI complex using PyGBe and APBS. Errors were calculated with respect to the corresponding extrapolated values (obtained from Richardson extrapolation). This result is part of the paper: —"A biomolecular electrostatics solver using Python, GPUs and boundary elements that can handle solvent-filled cavities and Stern layers", Christopher D. Cooper, Jaydeep P. Bardhan, L. A. Barba. <em>Comput. Phys. Comm.</em>, <strong>185</strong>(3):720–729 (March 2014). 10.1016/j.cpc.2013.10.028 // Preprint arXiv:1309.4018 PyGBe solves biomolecular electrostatics problems using an implicit-solvent model (Poisson-Boltzmann) and it uses GPU hardware for fast execution. It is written in Python, PyCUDA and CUDA. More information about the PyGBe code in: <em>—Validation of the PyGBe code for Poisson-Boltzmann equation with boundary element methods</em>. Christopher Cooper, Lorena A. Barba. figshare.<br>http://dx.doi.org/10.6084/m9.figshare.154331 <strong>Acknowledgement:</strong><br>This research is made possible by support from the Office of Naval Research, Applied Computational Analysis Program, N00014-11-1-0356. LAB also acknowledges support from NSF CAREER award OCI-1149784.
DOI: 10.6084/m9.figshare.799704
title: Binding energy of peptide-RNA complex with PyGBe and APBS

description: This file bundle includes data, figures and plotting scripts of solvation energy and binding energy calculations for peptide-RNA complex using PyGBe and APBS. Errors were calculated with respect to the corresponding extrapolated values (obtained from Richardson extrapolation). This result is part of the paper: —"A biomolecular electrostatics solver using Python, GPUs and boundary elements that can handle solvent-filled cavities and Stern layers", Christopher D. Cooper, Jaydeep P. Bardhan, L. A. Barba. <em>Comput. Phys. Comm.,</em> <strong>185</strong>(3):720–729 (March 2014). 10.1016/j.cpc.2013.10.028 // Preprint arXiv:1309.4018 PyGBe solves biomolecular electrostatics problems using an implicit-solvent model (Poisson-Boltzmann) and it uses GPU hardware for fast execution. It is written in Python, PyCUDA and CUDA. More information about the PyGBe code in: <em>—Validation of the PyGBe code for Poisson-Boltzmann equation with boundary element methods</em>. Christopher Cooper, Lorena A. Barba. figshare.<br>http://dx.doi.org/10.6084/m9.figshare.154331 <strong>Acknowledgement:</strong><br>This research is made possible by support from the Office of Naval Research, Applied Computational Analysis Program, N00014-11-1-0356. LAB also acknowledges support from NSF CAREER award OCI-1149784.
DOI: 10.6084/m9.figshare.799715
title: Gaussian Job Archive for F4S2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.799704.v1
title: Binding energy of peptide-RNA complex with PyGBe and APBS

description: This file bundle includes data, figures and plotting scripts of solvation energy and binding energy calculations for peptide-RNA complex using PyGBe and APBS. Errors were calculated with respect to the corresponding extrapolated values (obtained from Richardson extrapolation). This result is part of the paper: —"A biomolecular electrostatics solver using Python, GPUs and boundary elements that can handle solvent-filled cavities and Stern layers", Christopher D. Cooper, Jaydeep P. Bardhan, L. A. Barba. <em>Comput. Phys. Comm.,</em> <strong>185</strong>(3):720–729 (March 2014). 10.1016/j.cpc.2013.10.028 // Preprint arXiv:1309.4018 PyGBe solves biomolecular electrostatics problems using an implicit-solvent model (Poisson-Boltzmann) and it uses GPU hardware for fast execution. It is written in Python, PyCUDA and CUDA. More information about the PyGBe code in: <em>—Validation of the PyGBe code for Poisson-Boltzmann equation with boundary element methods</em>. Christopher Cooper, Lorena A. Barba. figshare.<br>http://dx.doi.org/10.6084/m9.figshare.154331 <strong>Acknowledgement:</strong><br>This research is made possible by support from the Office of Naval Research, Applied Computational Analysis Program, N00014-11-1-0356. LAB also acknowledges support from NSF CAREER award OCI-1149784.
DOI: 10.6084/m9.figshare.799715.v1
title: Gaussian Job Archive for F4S2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.