cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.2993812.v8
title: Generic stabilizability for time-delayed feedback control (Supplementary material)

description: Supplementary material and supporting code for the paper <br><br>Sieber J. 2016 Generic stabilizability for time-delayed feedback<br>control. Proc. R. Soc. A 20150593.<br>http://dx.doi.org/10.1098/rspa.2015.0593<br><br>arxiv preprint at http://arxiv.org/abs/1508.05671<br><br>
DOI: 10.6084/m9.figshare.2993812.v7
title: Generic stabilisability for time-delayed feedback control (Supplementary material)

description: Supplementary material and supporting code for the paper <br><br>Sieber J. 2016 Generic stabilizability for time-delayed feedback<br>control. Proc. R. Soc. A 20150593.<br>http://dx.doi.org/10.1098/rspa.2015.0593<br><br>arxiv preprint at http://arxiv.org/abs/1508.05671<br><br>
DOI: 10.6084/m9.figshare.2955931
title: Semester of Code Evaluation: Questionnaire for academic supervisors

description: This document presents the questionnaire filled by the academic supervisors in the Semester of Code process during the evaluation of the virtual placements performed.
DOI: 10.6084/m9.figshare.2956237
title: Hydria.jpg

description: Archaeology and Greek vase painting history: Naple 2422 Vase and Classical pottery description and <em>meaning</em> https://www.academia.edu/22470068/The_Kleophrades_Sack_of_Troy_on_Vivenzio_funerary_hydria_and_fragmented_skeletons_from_Veyrier
DOI: 10.6084/m9.figshare.2971957.v1
title: long & short term distribution comparison.xlsm

description: working file
DOI: 10.6084/m9.figshare.2953720
title: Semester of Code Evaluation: Questionnaire for students

description: This document presents the questionnaire filled by the students in the Semester of Code process during the evaluation of the virtual placements performed.
DOI: 10.6084/m9.figshare.2956237.v2
title: Hydria.jpg

description: Archaeology and Greek vase painting history: Naple 2422 Vase and Classical pottery description and <em>meaning</em> https://www.academia.edu/22470068/The_Kleophrades_Sack_of_Troy_on_Vivenzio_funerary_hydria_and_fragmented_skeletons_from_Veyrier
DOI: 10.6084/m9.figshare.2948377
title: Cellular resolution data from wild-type and reconstituted eve stripe 2 enhancer reporter constructs

description: Data accompanying Vincent et al. 2016. Files include the following:<br>pointclouds_costain.zip : Cellular resolution data from individual embryos containing reporter constructs for wild-type and reconstituted versions of the enhancer controlling the second stripe of the <i>even-skipped</i> expression pattern (<i>eve2</i>). Embryos were stained for <i>fushi tarasu (ftz) </i>in the coumarin channel and <i>LacZ </i>in the Cy3 channel. A <i>huckebein (hkb)</i> co-stain is also included in the Cy3 channel to normalize expression levels between lines (see Wunderlich, et al. 2014). Each Pointcloud file contains the xyz coordinates, <i>ftz</i> expression level, and <i>LacZ/hkb</i> expression level for every nucleus in the embryo. All embryos were stained with the same probes in the same batch.<br>atlas_costain.vpc : A cellular resolution gene expression atlas of an average <i>Drosophila melanogaster </i>embryo. Contains expression patterns generated by wild-type and reconstituted versions of <i>eve2</i>. Computational methods for atlas generation can be found in Fowlkes, et al. 2008. Pointclouds used to make the atlas are included in pointclouds_costain.zip. Cellular resolution data for <i>eve2 </i>regulators can be downloaded from the Berkeley Drosophila Transcription Network Project (http://bdtnp.lbl.gov/Fly-Net/bidatlas.jsp).<br>pointclouds_nocostain.zip : Cellular resolution data from individual embryos containing reporter constructs for wild-type and reconstituted versions of <i>eve2</i>. These embryos were not co-stained for <i>hkb</i>. <br>atlas_costain.vpc : A cellular resolution gene expression atlas of an average <i>Drosophila melanogaster </i>embryo. Contains expression patterns generated by wild-type and reconstituted versions of <i>eve2</i>. This atlas was generated from embryos that were not co-stained for <i>hkb</i>. <br><br><br><br>
DOI: 10.6084/m9.figshare.2949508
title: Full circumpolar migration ensures evolutionary unity in the Emperor penguin

description: - Consensus SNP calls dataset from RADseq data for the Emperor penguin.<br>Input files for the analyses described in Cristofari et al. 2016, "Full circumpolar migration ensures evolutionary unity in the Emperor penguin":<br>- Extended Bayesian Skyline Plot input files,- fastsimcoal2 analysis input files,- ngsAdmix genotype likelihood input file,- generic Structure / fastStructure input file,- Migrate-n analysis input files,
DOI: 10.6084/m9.figshare.2948377.v1
title: Cellular resolution data from wild-type and reconstituted eve stripe 2 enhancer reporter constructs

description: Data accompanying Vincent et al. 2016. Files include the following:<br>pointclouds_costain.zip : Cellular resolution data from individual embryos containing reporter constructs for wild-type and reconstituted versions of the enhancer controlling the second stripe of the <i>even-skipped</i> expression pattern (<i>eve2</i>). Embryos were stained for <i>fushi tarasu (ftz) </i>in the coumarin channel and <i>LacZ </i>in the Cy3 channel. A <i>huckebein (hkb)</i> co-stain is also included in the Cy3 channel to normalize expression levels between lines (see Wunderlich, et al. 2014). Each Pointcloud file contains the xyz coordinates, <i>ftz</i> expression level, and <i>LacZ/hkb</i> expression level for every nucleus in the embryo. All embryos were stained with the same probes in the same batch.<br>atlas_costain.vpc : A cellular resolution gene expression atlas of an average <i>Drosophila melanogaster </i>embryo. Contains expression patterns generated by wild-type and reconstituted versions of <i>eve2</i>. Computational methods for atlas generation can be found in Fowlkes, et al. 2008. Pointclouds used to make the atlas are included in pointclouds_costain.zip. Cellular resolution data for <i>eve2 </i>regulators can be downloaded from the Berkeley Drosophila Transcription Network Project (http://bdtnp.lbl.gov/Fly-Net/bidatlas.jsp).<br>pointclouds_nocostain.zip : Cellular resolution data from individual embryos containing reporter constructs for wild-type and reconstituted versions of <i>eve2</i>. These embryos were not co-stained for <i>hkb</i>. <br>atlas_costain.vpc : A cellular resolution gene expression atlas of an average <i>Drosophila melanogaster </i>embryo. Contains expression patterns generated by wild-type and reconstituted versions of <i>eve2</i>. This atlas was generated from embryos that were not co-stained for <i>hkb</i>. <br><br><br><br>
DOI: 10.6084/m9.figshare.2949508.v1
title: Full circumpolar migration ensures evolutionary unity in the Emperor penguin

description: - Consensus SNP calls dataset from RADseq data for the Emperor penguin.<br>Input files for the analyses described in Cristofari et al. 2016, "Full circumpolar migration ensures evolutionary unity in the Emperor penguin":<br>- Extended Bayesian Skyline Plot input files,- fastsimcoal2 analysis input files,- ngsAdmix genotype likelihood input file,- generic Structure / fastStructure input file,- Migrate-n analysis input files,
DOI: 10.6084/m9.figshare.2956237.v1
title: Hydria-The Cranbrook Academy of Arts, Bloomfield Hills copie.jpg

description: Archaeology and Greek vase painting history: Naple 2422 Vase and Classical pottery description and <em>meaning</em> https://www.academia.edu/22470068/The_Kleophrades_Sack_of_Troy_on_Vivenzio_funerary_hydria_and_fragmented_skeletons_from_Veyrier
DOI: 10.6084/m9.figshare.2930590
title: MPT.xlsx

description: portfolio optimization<br>
DOI: 10.6084/m9.figshare.2951263.v1
title: UNH-RVAT 3-D Spalart--Allmaras RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions with the Spalart--Allmaras RANS model in OpenFOAM 2.3.x (590d57f32fed). See link below for case files (SpalartAllmaras branch), which include a script for downloading and extracting, as well as scripts for post-processing.
DOI: 10.6084/m9.figshare.2930590.v1
title: MPT.xlsx

description: portfolio optimization<br>
DOI: 10.6084/m9.figshare.2896858
title: Twitter archive from the People in Disasters Conference #PIDC2016, 24-27 February 2016

description: This file contains a data set of 280 tweets tagged with #PIDC2016 (case not sensitive) that were published on Twitter between 23/02/2016 10:01:34 and 26/02/2016 GMT. This file was created and shared by Sarah Gallagher @sarahlibrarina (University of Otago, Dunedin, New Zealand) with a Creative Commons Attribution license (CC-BY) to encourage research in scholarly communication and for educational purposes. The Tweets contained in this file were collected using Martin Hawksey’s [@mhawksey] TAGS 6.0 http://tags.hawksey.info/ Spam tweets have been manually removed. Despite this intervention data may require further refining. The contents of each Tweet are responsibility of the original authors. This data set has been shared “as is”, for educational and research purposes. As noted by Priego (2014) “both research and experience show that the Twitter search API isn't 100% reliable. Large tweet volumes affect the search collection process. The API might "over-represent the more central users", not offering "an accurate picture of peripheral activity" (González-Bailón, Sandra, et al. 2012).” Therefore there is no guarantee that this file all Tweets tagged with (#PIDC2016) during the indicated period. This dataset is shared to encourage open research into scholarly activity on Twitter. If you use or refer to this data in any way please cite using the preferred citation above. Contact: @sarahlibrarina
DOI: 10.6084/m9.figshare.2951263.v2
title: UNH-RVAT 3-D Spalart--Allmaras RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions with the Spalart--Allmaras RANS model in OpenFOAM 2.3.x (590d57f32fed). See link below for case files (note: use the `SpalartAllmaras` branch), which include a script for downloading and extracting, as well as scripts for post-processing.
DOI: 10.6084/m9.figshare.2896057
title: Lortie meta-figshare stats 26.02.2016.xlsx

description: Here is a meta-scrape of the reported usages statistics for datasets on figshare as reported by figshare.
DOI: 10.6084/m9.figshare.2896858.v1
title: Twitter archive from the People in Disasters Conference #PIDC2016, 24-27 February 2016

description: This file contains a data set of 280 tweets tagged with #PIDC2016 (case not sensitive) that were published on Twitter between 23/02/2016 10:01:34 and 26/02/2016 GMT. This file was created and shared by Sarah Gallagher @sarahlibrarina (University of Otago, Dunedin, New Zealand) with a Creative Commons Attribution license (CC-BY) to encourage research in scholarly communication and for educational purposes. The Tweets contained in this file were collected using Martin Hawksey’s [@mhawksey] TAGS 6.0 http://tags.hawksey.info/ Spam tweets have been manually removed. Despite this intervention data may require further refining. The contents of each Tweet are responsibility of the original authors. This data set has been shared “as is”, for educational and research purposes. As noted by Priego (2014) “both research and experience show that the Twitter search API isn't 100% reliable. Large tweet volumes affect the search collection process. The API might "over-represent the more central users", not offering "an accurate picture of peripheral activity" (González-Bailón, Sandra, et al. 2012).” Therefore there is no guarantee that this file all Tweets tagged with (#PIDC2016) during the indicated period. This dataset is shared to encourage open research into scholarly activity on Twitter. If you use or refer to this data in any way please cite using the preferred citation above. Contact: @sarahlibrarina
DOI: 10.6084/m9.figshare.2896057.v1
title: Lortie meta-figshare stats 26.02.2016.xlsx

description: Here is a meta-scrape of the reported usages statistics for datasets on figshare as reported by figshare.
DOI: 10.6084/m9.figshare.2951263.v3
title: UNH-RVAT 3-D Spalart--Allmaras RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions with the Spalart--Allmaras RANS model in OpenFOAM 2.3.x (590d57f32fed). See link below for case files (note: use the `SpalartAllmaras` branch), which include a script for downloading and extracting, as well as scripts for post-processing.
DOI: 10.6084/m9.figshare.2951263.v4
title: UNH-RVAT 3-D Spalart--Allmaras RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions with the Spalart--Allmaras RANS model in OpenFOAM 2.3.x (590d57f32fed). See link below for case files (note: use the `SpalartAllmaras` branch), which include a script for downloading and extracting, as well as scripts for post-processing.
DOI: 10.6084/m9.figshare.2951263.v5
title: UNH-RVAT 3-D Spalart--Allmaras RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions with the Spalart--Allmaras RANS model in OpenFOAM 2.3.x (590d57f32fed). See link below for case files (note: use the `SpalartAllmaras` branch), which include a script for downloading and extracting, as well as scripts for post-processing.
DOI: 10.6084/m9.figshare.2889625
title: Spatial distribution of filament elasticity determines the migratory behaviors of a cell

description: Any cellular response leading to morphological changes is highly tuned to balance the force generated from structural reorganization, provided by actin cytoskeleton. Actin filaments serve as the backbone of intracellular force, and transduce external mechanical signal via focal adhesion complex into the cell. During migration, cells not only undergo molecular changes but also rapid mechanical modulation. Here we focus on determining, the role of spatial distribution of mechanical changes of actin filaments in epithelial, mesenchymal, fibrotic and cancer cells with non-migration, directional migration, and non-directional migration behaviors using the atomic force microscopy. We found 1) non-migratory cells only generated one type of filament elasticity, 2) cells generating spatially distributed two types of filament elasticity showed directional migration, and 3) pathologic cells that autonomously generated two types of filament elasticity without spatial distribution were actively migrating non-directionally. The demonstration of spatial regulation of filament elasticity of different cell types at the nano-scale highlights the coupling of cytoskeletal function with physical characters at the sub-cellular level, and provides new research directions for migration related disease.
DOI: 10.6084/m9.figshare.2889625.v1
title: Spatial distribution of filament elasticity determines the migratory behaviors of a cell

description: Any cellular response leading to morphological changes is highly tuned to balance the force generated from structural reorganization, provided by actin cytoskeleton. Actin filaments serve as the backbone of intracellular force, and transduce external mechanical signal via focal adhesion complex into the cell. During migration, cells not only undergo molecular changes but also rapid mechanical modulation. Here we focus on determining, the role of spatial distribution of mechanical changes of actin filaments in epithelial, mesenchymal, fibrotic and cancer cells with non-migration, directional migration, and non-directional migration behaviors using the atomic force microscopy. We found 1) non-migratory cells only generated one type of filament elasticity, 2) cells generating spatially distributed two types of filament elasticity showed directional migration, and 3) pathologic cells that autonomously generated two types of filament elasticity without spatial distribution were actively migrating non-directionally. The demonstration of spatial regulation of filament elasticity of different cell types at the nano-scale highlights the coupling of cytoskeletal function with physical characters at the sub-cellular level, and provides new research directions for migration related disease.
DOI: 10.6084/m9.figshare.2888524
title: BSM.xlsm

description: working files
DOI: 10.6084/m9.figshare.2951263.v6
title: UNH-RVAT 3-D Spalart--Allmaras RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions with the Spalart--Allmaras RANS model in OpenFOAM 2.3.x (590d57f32fed). See link below for case files (note: use the `SpalartAllmaras` branch), which include a script for downloading and extracting, as well as scripts for post-processing.
DOI: 10.6084/m9.figshare.2888524.v1
title: BSM.xlsm

description: working files
DOI: 10.6084/m9.figshare.2889622
title: Cdc45 is limiting for replication initiation in humans

description: Cdc45 is an essential protein that together with Mcm2-7 and GINS forms the eukaryotic replicative helicase CMG. Cdc45 seems to be rate limiting for the initial unwinding or firing of replication origins. In line with this view, Cdc45-overexpressing cells fired at least twice as many origins as control cells. However, these cells displayed an about 2-fold diminished fork elongation rate, a pronounced asymmetry of replication fork extension, and an early S phase arrest. This was accompanied by H2AX-phosphorylation and subsequent apoptosis. Unexpectedly, we did not observe increased ATR/Chk1 signaling but rather a mild ATM/Chk2 response. In addition, we detected accumulation of long stretches of single-stranded DNA, a hallmark of replication catastrophe. We conclude that increased origin firing by upregulated Cdc45 caused exhaustion of the single-strand binding protein RPA, which in consequence diminished the ATR/Chk1 response; the subsequently occurring fork breaks led to an ATM/Chk2 mediated phosphorylation of H2AX and eventually to apoptosis.
DOI: 10.6084/m9.figshare.2889622.v1
title: Cdc45 is limiting for replication initiation in humans

description: Cdc45 is an essential protein that together with Mcm2-7 and GINS forms the eukaryotic replicative helicase CMG. Cdc45 seems to be rate limiting for the initial unwinding or firing of replication origins. In line with this view, Cdc45-overexpressing cells fired at least twice as many origins as control cells. However, these cells displayed an about 2-fold diminished fork elongation rate, a pronounced asymmetry of replication fork extension, and an early S phase arrest. This was accompanied by H2AX-phosphorylation and subsequent apoptosis. Unexpectedly, we did not observe increased ATR/Chk1 signaling but rather a mild ATM/Chk2 response. In addition, we detected accumulation of long stretches of single-stranded DNA, a hallmark of replication catastrophe. We conclude that increased origin firing by upregulated Cdc45 caused exhaustion of the single-strand binding protein RPA, which in consequence diminished the ATR/Chk1 response; the subsequently occurring fork breaks led to an ATM/Chk2 mediated phosphorylation of H2AX and eventually to apoptosis.
DOI: 10.6084/m9.figshare.2951263.v7
title: UNH-RVAT 3-D Spalart--Allmaras RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions with the Spalart--Allmaras RANS model in OpenFOAM 2.3.x (590d57f32fed). See link below for case files (note: use the `SpalartAllmaras` branch), which include a script for downloading and extracting, as well as scripts for post-processing.
DOI: 10.6084/m9.figshare.2888131
title: Analysis of nanoparticle–protein coronas formed <i>in vitro</i> between nanosized welding particles and nasal lavage proteins

description: Welding fumes include agglomerated particles built up of primary nanoparticles. Particles inhaled through the nose will to some extent be deposited in the protein-rich nasal mucosa, and a protein corona will be formed around the particles. The aim was to identify the protein corona formed between nasal lavage proteins and four types of particles with different parameters. Two of the particles were formed and collected during welding and two were manufactured iron oxides. When nasal lavage proteins were added to the particles, differences were observed in the sizes of the aggregates that were formed. Measurements showed that the amount of protein bound to particles correlated with the relative size increase of the aggregates, suggesting that the surface area was associated with the binding capacity. However, differences in aggregate sizes were detected when nasal proteins were added to UF<sub>WF</sub> and Fe<sub>2</sub>O<sub>3</sub> particles (having similar agglomerated size) suggesting that yet parameters other than size determine the binding. Relative quantitative mass spectrometric and gel-based analyses showed differences in the protein content of the coronas. High-affinity proteins were further assessed for network interactions. Additional experiments showed that the inhibitory function of secretory leukocyte peptidase inhibitor, a highly abundant nasal protein, was influenced by particle binding suggesting that an understanding of protein function following particle binding is necessary to properly evaluate pathophysiological events. Our results underscore the importance of including particles collected from real working environments when studying the toxic effects of particles because these effects might be mediated by the protein corona.
DOI: 10.6084/m9.figshare.2888131.v1
title: Analysis of nanoparticle–protein coronas formed <i>in vitro</i> between nanosized welding particles and nasal lavage proteins

description: Welding fumes include agglomerated particles built up of primary nanoparticles. Particles inhaled through the nose will to some extent be deposited in the protein-rich nasal mucosa, and a protein corona will be formed around the particles. The aim was to identify the protein corona formed between nasal lavage proteins and four types of particles with different parameters. Two of the particles were formed and collected during welding and two were manufactured iron oxides. When nasal lavage proteins were added to the particles, differences were observed in the sizes of the aggregates that were formed. Measurements showed that the amount of protein bound to particles correlated with the relative size increase of the aggregates, suggesting that the surface area was associated with the binding capacity. However, differences in aggregate sizes were detected when nasal proteins were added to UF<sub>WF</sub> and Fe<sub>2</sub>O<sub>3</sub> particles (having similar agglomerated size) suggesting that yet parameters other than size determine the binding. Relative quantitative mass spectrometric and gel-based analyses showed differences in the protein content of the coronas. High-affinity proteins were further assessed for network interactions. Additional experiments showed that the inhibitory function of secretory leukocyte peptidase inhibitor, a highly abundant nasal protein, was influenced by particle binding suggesting that an understanding of protein function following particle binding is necessary to properly evaluate pathophysiological events. Our results underscore the importance of including particles collected from real working environments when studying the toxic effects of particles because these effects might be mediated by the protein corona.
DOI: 10.6084/m9.figshare.2951263.v8
title: UNH-RVAT 3-D Spalart--Allmaras RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions with the Spalart--Allmaras RANS model in OpenFOAM 2.3.x (590d57f32fed). See link below for case files (note: use the `SpalartAllmaras` branch), which include a script for downloading and extracting, as well as scripts for post-processing.