cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3980472
title: Hancock, P.A., White, V.L., Ritchie, S.A.,Hoffmann, A.A. and Godfray, H.C.J. 2016 Predicting Wolbachia invasion dynamics in Aedes aegypti populations using models of density-dependent demographic traits. BMC Biology. C++ computer code for implementing the population dynamic model described in Hancock et al. 2016 BMC Biology

description: gyp_sim.cpp (version 04/10/2016) was developed by Dr Penelope A. Hancockgyp_sim.cpp comprises C++ code for implementing the modelof mosquito-Wolbachia dynamics developed in Hancock et al. 2016,"Predicting Wolbachia invasion dynamics in Aedes aegypti populations usingmodels of density-dependent demographic traits", BMC Biology.<br>To run gyp_sim use the command gyp_sim.exe<br>The file gyp_sim_inits.txt contains the following inputs:<br>Cohort_means.txt (a file for storing the mean development times of uninfected larvae in each cohort)Cohort_means_wolb.txt (a file for storing the mean development times of infected larvae in each cohort)Cohort_stds.txt (a file for storing the standard deviations of the development times of uninfected larvae in each cohort)Cohort_stds_wolb.txt (a file for storing the standard deviations of the development times of infected larvae in each cohort)mu_p.txt (a file for storing the number of uninfected pupae that eclose on each day)L_file.txt (a file for storing the number of uninfected larvae present on each day)A_file.txt (a file for storing the number of uninfected adults present on each day)mu_p_wolb.txt (a file for storing the number of infected pupae that eclose on each day)L_wolb_file.txt (a file for storing the number of infected larvae present on each day)A_wolb_file.txt (a file for storing the number of infected adults present on each day)FreqA2_file.txt (a file for storing the Wolbachia frequency on the final day of release)lambda.txt (a file for storing the per-capita female fecundity at the time that each cohort is hatched)release_size.txt (a file for storing the size of each Wolbachia release)700 (the day of the first release)0.1 (additional density-INdependent daily mortality experienced by adults In the field environment)0.1 (additional density-INdependent daily mortality experienced by larvae in the field environment)<br>
DOI: 10.7910/dvn/v1rjpf/dzk2zq
title: snk20160723_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3980463
title: Outcomes of SAVE-SD 2015 and 2016 questionnaires on RASH and analysis of RDF annotations in the RASH papers.

description: This dataset contains all the source materials and the data collected for the evaluation of RASH (Research Articles in Simplified HTML), which is presented in the paper:<br>Peroni, S., Osborne, F., Di Iorio, A., Nuzzolese, A., Poggi, F., Vitali, F., Motta, E. (2017). Research Articles in Simplified HTML: a Web-first format for HTML-based scholarly articles. https://w3id.org/people/essepuntato/papers/rash-peerj2016.html<br>submitted to the PeerJ Computer Science.<br><br>In particular this archive contains seven items:- the file "README.txt" (this file);- the directory "save-sd2015", containing the source of six RASH articles submitted to SAVE-SD 2015 and their related RDF statements extracted from them and stored as Turtle files;- the directory "save-sd2016", containing the source of five RASH articles submitted to SAVE-SD 2015 and their related RDF statements extracted from them and stored as Turtle files;- the directory "stats", containing CSVf files with data about the RDF statements extracted from the RASH papers presented in the two edition of SAVE-SD.- the directory "script" containing the Python scripts creating the CSV files;- the file "script.sh" that runs the computation for creating all the statistics stored in the directory "stats";- the directory "questionnaires", containing four CSV files reporting the questionnaires filled in by authors and reviewers of RASH papers published in the SAVE-SD 2015 and SAVE-SD 2016 workshops.<br>In particular, the "stats" directory contains two directories describing the data about the statements of the RASH papers of SAVE-SD 2015 ("2015") and of SAVE-SD 2016 ("2016"). A summary of all these data is provided in the directory "tot".<br>Each of these directories contains four distinct CSV files:- "stats_short.csv" contains all the numeric data related to the vocabularies used in the statements and the way they have been involved in the RASH papers;- "stats.csv" extends the previous CSV file by adding also all the information related to each of the entities involved per vocabulary;- "stats_perc.csv" contains the percentages of the vocabularies used in the statements and the way they have been involved in the RASH papers;- "stats_short_perc.csv" extends the previous CSV file by adding also all the information related to each of the entities involved per vocabulary.<br>In the CSV tables, the last columns are dedicated to some metrics calculated starting from the values specified for each vocabulary/entity involved in the papers. In particular:- "TOTAL" is the sum of all the statements indicated in a row;- "mean" is the arithmetic mean of all the statements indicated in a row;- "std" is the standard deviation of related to the arithmetic mean;- "sqrt" is the sum of all the square root values of all the statements indicated in a row;- "log" is the sum of all the natural logarithm values of all the statements indicated in a row.<br><br>For any question about the data please contact francesco.osborne@open.ac.uk or silvio.peroni@unibo.it
DOI: 10.6084/m9.figshare.3980472.v1
title: Hancock, P.A., White, V.L., Ritchie, S.A.,Hoffmann, A.A. and Godfray, H.C.J. 2016 Predicting Wolbachia invasion dynamics in Aedes aegypti populations using models of density-dependent demographic traits. BMC Biology. C++ computer code for implementing the population dynamic model described in Hancock et al. 2016 BMC Biology

description: gyp_sim.cpp (version 04/10/2016) was developed by Dr Penelope A. Hancockgyp_sim.cpp comprises C++ code for implementing the modelof mosquito-Wolbachia dynamics developed in Hancock et al. 2016,"Predicting Wolbachia invasion dynamics in Aedes aegypti populations usingmodels of density-dependent demographic traits", BMC Biology.<br>To run gyp_sim use the command gyp_sim.exe<br>The file gyp_sim_inits.txt contains the following inputs:<br>Cohort_means.txt (a file for storing the mean development times of uninfected larvae in each cohort)Cohort_means_wolb.txt (a file for storing the mean development times of infected larvae in each cohort)Cohort_stds.txt (a file for storing the standard deviations of the development times of uninfected larvae in each cohort)Cohort_stds_wolb.txt (a file for storing the standard deviations of the development times of infected larvae in each cohort)mu_p.txt (a file for storing the number of uninfected pupae that eclose on each day)L_file.txt (a file for storing the number of uninfected larvae present on each day)A_file.txt (a file for storing the number of uninfected adults present on each day)mu_p_wolb.txt (a file for storing the number of infected pupae that eclose on each day)L_wolb_file.txt (a file for storing the number of infected larvae present on each day)A_wolb_file.txt (a file for storing the number of infected adults present on each day)FreqA2_file.txt (a file for storing the Wolbachia frequency on the final day of release)lambda.txt (a file for storing the per-capita female fecundity at the time that each cohort is hatched)release_size.txt (a file for storing the size of each Wolbachia release)700 (the day of the first release)0.1 (additional density-INdependent daily mortality experienced by adults In the field environment)0.1 (additional density-INdependent daily mortality experienced by larvae in the field environment)<br>
DOI: 10.7910/dvn/v1rjpf/vipejw
title: snk20161023_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/pcjiir
title: snk20160317_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/nm8zys
title: snk20160701_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3980463.v1
title: RASH evaluation

description: This dataset contains the data collected for the evaluation of RASH (Research Articles in Simplified HTML), which is presented in the paper 'Research Articles in Simplified HTML: a Web-first format for HTML-based scholarly articles'.<br>In particular, it includes:<br>1) Four CSV files reporting the surveys filled in by authors and reviewers of RASH papers published in the SAVE-SD 2015 and SAVE-SD 2016 workshops:- survey_authors_2015- survey_authors_2016- survey_reviewers_2015- survey_reviewers_2016<br>2) Four CSV files presenting the more frequent entities and vocabularies included in the RASH papers published in SAVE-SD 2015 and SAVE-SD 2016 workshops:- entities_analysis_2015.csv- entities_analysis_2016.csv- vocabularies_analysis_2015.csv- vocabularies_analysis_2016.csv <br>For any question about the data please contact francesco.osborne@open.ac.uk or silvio.peroni@unibo.it<br>
DOI: 10.7910/dvn/v1rjpf/e9qh0s
title: snk20150525_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3980463.v2
title: RASH evaluation

description: This dataset contains the data collected for the evaluation of RASH (Research Articles in Simplified HTML), which is presented in the paper 'Research Articles in Simplified HTML: a Web-first format for HTML-based scholarly articles'.<br>In particular, it includes:<br>1) Four CSV files reporting the surveys filled in by authors and reviewers of RASH papers published in the SAVE-SD 2015 and SAVE-SD 2016 workshops:- survey_authors_2015- survey_authors_2016- survey_reviewers_2015- survey_reviewers_2016<br>2) Four CSV files presenting the more frequent entities and vocabularies included in the RASH papers published in SAVE-SD 2015 and SAVE-SD 2016 workshops:- entities_analysis_2015.csv- entities_analysis_2016.csv- vocabularies_analysis_2015.csv- vocabularies_analysis_2016.csv <br>For any question about the data please contact francesco.osborne@open.ac.uk or silvio.peroni@unibo.it<br>
DOI: 10.7910/dvn/v1rjpf/w9wsd5
title: snk20160326_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3980463.v3
title: Outcomes of SAVE-SD 2015 and 2016 questionnaires on RASH and evaluation material and outcomes of the analysis of RDF annotations in the RASH papers.

description: This dataset contains the data collected for the evaluation of RASH (Research Articles in Simplified HTML), which is presented in the paper 'Research Articles in Simplified HTML: a Web-first format for HTML-based scholarly articles'.<br>In particular, it includes:<br>1) Four CSV files reporting the surveys filled in by authors and reviewers of RASH papers published in the SAVE-SD 2015 and SAVE-SD 2016 workshops:- survey_authors_2015- survey_authors_2016- survey_reviewers_2015- survey_reviewers_2016<br>2) Four CSV files presenting the more frequent entities and vocabularies included in the RASH papers published in SAVE-SD 2015 and SAVE-SD 2016 workshops:- entities_analysis_2015.csv- entities_analysis_2016.csv- vocabularies_analysis_2015.csv- vocabularies_analysis_2016.csv <br>For any question about the data please contact francesco.osborne@open.ac.uk or silvio.peroni@unibo.it<br>
DOI: 10.7910/dvn/v1rjpf/wvuuqz
title: snk20150202_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3980463.v5
title: Outcomes of SAVE-SD 2015 and 2016 questionnaires on RASH and analysis of RDF annotations in the RASH papers.

description: This dataset contains all the source materials and the data collected for the evaluation of RASH (Research Articles in Simplified HTML), which is presented in the paper:<br>Peroni, S., Osborne, F., Di Iorio, A., Nuzzolese, A., Poggi, F., Vitali, F., Motta, E. (2017). Research Articles in Simplified HTML: a Web-first format for HTML-based scholarly articles. https://w3id.org/people/essepuntato/papers/rash-peerj2016.html<br>submitted to the PeerJ Computer Science.<br><br>In particular this archive contains seven items:- the file "README.txt" (this file);- the directory "save-sd2015", containing the source of six RASH articles submitted to SAVE-SD 2015 and their related RDF statements extracted from them and stored as Turtle files;- the directory "save-sd2016", containing the source of five RASH articles submitted to SAVE-SD 2015 and their related RDF statements extracted from them and stored as Turtle files;- the directory "stats", containing CSVf files with data about the RDF statements extracted from the RASH papers presented in the two edition of SAVE-SD.- the directory "script" containing the Python scripts creating the CSV files;- the file "script.sh" that runs the computation for creating all the statistics stored in the directory "stats";- the directory "questionnaires", containing four CSV files reporting the questionnaires filled in by authors and reviewers of RASH papers published in the SAVE-SD 2015 and SAVE-SD 2016 workshops.<br>In particular, the "stats" directory contains two directories describing the data about the statements of the RASH papers of SAVE-SD 2015 ("2015") and of SAVE-SD 2016 ("2016"). A summary of all these data is provided in the directory "tot".<br>Each of these directories contains four distinct CSV files:- "stats_short.csv" contains all the numeric data related to the vocabularies used in the statements and the way they have been involved in the RASH papers;- "stats.csv" extends the previous CSV file by adding also all the information related to each of the entities involved per vocabulary;- "stats_perc.csv" contains the percentages of the vocabularies used in the statements and the way they have been involved in the RASH papers;- "stats_short_perc.csv" extends the previous CSV file by adding also all the information related to each of the entities involved per vocabulary.<br>In the CSV tables, the last columns are dedicated to some metrics calculated starting from the values specified for each vocabulary/entity involved in the papers. In particular:- "TOTAL" is the sum of all the statements indicated in a row;- "mean" is the arithmetic mean of all the statements indicated in a row;- "std" is the standard deviation of related to the arithmetic mean;- "sqrt" is the sum of all the square root values of all the statements indicated in a row;- "log" is the sum of all the natural logarithm values of all the statements indicated in a row.<br><br>For any question about the data please contact francesco.osborne@open.ac.uk or silvio.peroni@unibo.it
DOI: 10.6084/m9.figshare.3980463.v4
title: Outcomes of SAVE-SD 2015 and 2016 questionnaires on RASH and analysis of RDF annotations in the RASH papers.

description: This dataset contains the data collected for the evaluation of RASH (Research Articles in Simplified HTML), which is presented in the paper 'Research Articles in Simplified HTML: a Web-first format for HTML-based scholarly articles'.<br>In particular, it includes:<br>1) Four CSV files reporting the surveys filled in by authors and reviewers of RASH papers published in the SAVE-SD 2015 and SAVE-SD 2016 workshops:- survey_authors_2015- survey_authors_2016- survey_reviewers_2015- survey_reviewers_2016<br>2) Four CSV files presenting the more frequent entities and vocabularies included in the RASH papers published in SAVE-SD 2015 and SAVE-SD 2016 workshops:- entities_analysis_2015.csv- entities_analysis_2016.csv- vocabularies_analysis_2015.csv- vocabularies_analysis_2016.csv <br>For any question about the data please contact francesco.osborne@open.ac.uk or silvio.peroni@unibo.it<br>
DOI: 10.7910/dvn/v1rjpf/gk9idv
title: snk20151229_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/2spglk
title: snk20150331_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/ited7m
title: snk20150310_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3980346
title: Supplementary Material for: Uremic Toxin-Producing Gut Microbiota in Rats with Chronic Kidney Disease

description: <b><i>Background:</i></b> In patients with chronic kidney disease (CKD), many metabolites of gut microbiota retain in the body as uremic toxins (UTs). However, the kinds of bacteria producing UTs are rarely discussed. <b><i>Methods:</i></b> We analyzed UT production and the composition of gut microbiota in CKD rats and cecectomized rats. AST-120, a spherical carbon adsorbent, was administrated to evaluate how the precursors of UT affect gut microbiota. Serum and urine levels of UTs were quantified by liquid chromatography/electrospray ionization-tandem mass spectrometry. Gut microbiota were analyzed using 454-pyrosequencing of the 16S rRNA gene. Operational taxonomic unit (OTU) clustering and UniFrac analysis were performed to compare gut microbiota among the groups. <b><i>Results:</i></b> Serum and urine levels of indoxyl sulfate and phenyl sulfate were higher in CKD versus control rats (p &lt; 0.05). AST-120 administration decreased UT production (p &lt; 0.01) and changed overall gut microbiota composition in CKD rats. UT urinary excretion and gut microbiota composition changed in cecectomized rats, with the relative abundance of <i>Clostridia</i>- and <i>Bacteroidia</i>-affiliated species being significantly reduced (p &lt; 0.01). We identified candidate indole- and phenol-producing intestinal microbiota, 3 <i>Clostridia</i>, and 2 <i>Bacteroidia</i>. These OTUs have a tryptophanase/tyrosine phenol-lyase gene in the closest sequenced genome out of the OTUs declined following cecectomy. <b><i>Conclusion:</i></b> Our data suggest that UT production is correlated with a subset of indigenous gut microbiota. However, UT may be induced by other non-symbiotic microbiota that are influenced by factors other than microbiota populations. The relationship between specific microbiota and UTs in patients requires further clarification.
DOI: 10.6084/m9.figshare.3980349
title: Bromeliad predator phylogeny

description: This Newick tree contains data on the evolutionary relationships and divergence times, based on published phylogenies.<br><br>We included phylogenetic information in our analyses of all three datasets. We obtained this phylogenetic information first from classification alone. Next we added information about the age of each node from timetree.org, an online database of published molecular time estimates. The timetree online database collects information from multiple independent phylogenetic studies. These studies provide independent estimates of the age of the most recent common ancestor for two lineages. Lineages that diverged a long time ago have been dated by multiple studies; for such nodes we used the median age. All internal nodes were dated by at least one study, however data was unavailable for the youngest nodes (i.e. tips) of the tree. For these nodes, either a lack of taxonomic information (e.g. Tabanidae) or a lack of phylogenetic study (e.g. <em>Leptagrion</em>) prevented more information from being included. These branches were left unresolved (i.e., as polytomies) and were all assigned identical, arbitrary and short branch lengths (15 Mya). The result is a phylogeny that closely resembles the qualitative, taxonomy-based tree with which we began. Because the node ages between our major predators (leeches, tabanids and odonata) are so deep, variation among studies in the estimated age of these nodes was minor compared to the differences between them. ​I obtained these estimates from Timetree.org in July 2013<br>
DOI: 10.7910/dvn/v1rjpf/ayqdx9
title: snk20161215_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3980349.v1
title: Bromeliad predator phylogeny

description: This Newick tree contains data on the evolutionary relationships and divergence times, based on published phylogenies.<br><br>We included phylogenetic information in our analyses of all three datasets. We obtained this phylogenetic information first from classification alone. Next we added information about the age of each node from timetree.org, an online database of published molecular time estimates. The timetree online database collects information from multiple independent phylogenetic studies. These studies provide independent estimates of the age of the most recent common ancestor for two lineages. Lineages that diverged a long time ago have been dated by multiple studies; for such nodes we used the median age. All internal nodes were dated by at least one study, however data was unavailable for the youngest nodes (i.e. tips) of the tree. For these nodes, either a lack of taxonomic information (e.g. Tabanidae) or a lack of phylogenetic study (e.g. <em>Leptagrion</em>) prevented more information from being included. These branches were left unresolved (i.e., as polytomies) and were all assigned identical, arbitrary and short branch lengths (15 Mya). The result is a phylogeny that closely resembles the qualitative, taxonomy-based tree with which we began. Because the node ages between our major predators (leeches, tabanids and odonata) are so deep, variation among studies in the estimated age of these nodes was minor compared to the differences between them. ​I obtained these estimates from Timetree.org in July 2013<br>
DOI: 10.7910/dvn/v1rjpf/a9rtkr
title: snk20160908_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/prspzy
title: snk20161025_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/sawcvy
title: snk20150625_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/jcjjls
title: snk20150122_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3980256
title: Awareness of OER/OEP in HEIs in Scotland

description: The Open Educational Practices in Scotland (OEPS) Project conducted a survey to find out about the level of awareness of open educational resources (OER) and open educational practices (OEP) among HE institutions in Scotland. In total 235 valid responses were collected in a five-week period from 19<sup>th</sup> October 2015 to 23<sup>rd</sup> November 2015.
DOI: 10.7910/dvn/v1rjpf/kmpmhg
title: snk20160121_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3980256.v1
title: Awareness of OER/OEP in HEIs in Scotland

description: The Open Educational Practices in Scotland (OEPS) Project conducted a survey to find out about the level of awareness of open educational resources (OER) and open educational practices (OEP) among HE institutions in Scotland. In total 235 valid responses were collected in a five-week period from 19<sup>th</sup> October 2015 to 23<sup>rd</sup> November 2015.
DOI: 10.7910/dvn/v1rjpf/ri0r7h
title: snk20161017_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/oppps5
title: snk20150919_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3980175
title: MRI data for SciRep

description: Anonymized and skull-stripped MRI data (T1ce, FLAIR, R2', T2, T2*, CBV, rOEF) used for multi-parametric WHO grade prediction in newly diagnosed glioma in the manuscript "Multiparametric MRI-based differentiation of WHO grade II/III glioma and WHO grade IV glioblastoma" (Scientific Reports, Wiestler et al.)
DOI: 10.7910/dvn/v1rjpf/21y421
title: snk20150920_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3980184
title: HDLEC siRNA migration primary screen images

description: Images from high content genome-wide siRNA screen of lymphatic endothelial cell migration<br><br><b>File names:</b><br>Each folder is named according to the following convention:<br><br>(YYMMDD)(initials)(celltype)_(dharmacon plate #)(VCFG library freeze version 'A' or 'C')_(screen plate #)(technical rep 'A' or 'B')_(t00 or t24)<br><br>eg. 110131SWLEC_11024A_001A_t00<br><br>Each folder contains 96x 16-bit TIF images (ie from one plate) labelled with plate number and 'Well_A01' through to 'Well_H12', followed by the gene targeted by siRNA.<br><br>16-bit TIF images require specialised image analysis software to open correctly, such as the freely available ImageJ package.<br><br><b>Plate layout:</b><br>For detailed mapping of siRNA layout, please see Pubchem entry AID1159578 which includes migration data for the screen.<br><br><br><br>
DOI: 10.7910/dvn/v1rjpf/epxser
title: snk20160603_03.txt.gz

description: :unav