cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1016997.v2
title: A new specimen of the temnospondyl <i>Australerpeton cosgriffi</i> from the late Permian of Brazil (Rio do Rasto Formation, Paraná Basin): comparative anatomy and phylogenetic relationships

description: ABSTRACTA new temnospondyl specimen from the Rio do Rasto Formation (late Permian, Paraná Basin) of south Brazil is composed of a left mandible, right pelvis, femur, tibia, and fibula. Preserved lower jaws are rare for <i>Australerpeton cosgriffi</i>, and the weak ossification of the temnospondyl postcranium renders their preservation generally uncommon. A detailed comparative description of the material allowed its assignment to <i>Australerpeton cosgriffi</i>, and yielded new information about the morphology of mandible, pelvis, and hind limb of that taxon. This long-snouted temnospondyl has uncertain affinities and has been assigned either to stereospondyl Rhinesuchidae or to archegosaurid Platyoposaurinae. Reassessment of the phylogenetic placement of <i>Australerpeton cosgriffi</i>, with information drawn from the new specimen, confirms a basal stereospondyl position, between <i>Peltobatrachus pustulatus</i> and Rhinesuchidae. The synapomorphies shared with other stereospondyls include tabular and exoccipital contacting in the paroccipital process; parasphenoid articulates with corpus of the pterygoid forming a broad contact along the lateral margins of the parasphenoid plate; internal carotid passes through the dorsal surface of the parasphenoid plate; and parasphenoid denticles field enlarged to a transverse ‘belt’ extending between the pterygoid-parasphenoid articulations. Accordingly, <i>Australerpeton cosgriffi</i> represents one of the first stereospondyls, and the oldest long-snouted member of the group. The Paraná Basin can be included within the stereospondyl ancestral range, and dispersion and diversification of this clade appears to have happened before the Permo-Triassic boundary.SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at http://www.tandfonline.com/UJVP.
DOI: 10.6084/m9.figshare.1015787
title: Animal and Plant Phylogenies

description: Phylogenies associated with a paper in review in Plant Ecology. There is a zip file of animal trees and one for plant trees. All are in newick format. Description of tree creation: <strong>* Plants</strong> Plant phylogenies were built using Phylomatic (see http://phylodiversity.net/phylomatic; Webb & Donoghue 2004). Phylomatic is an online interface to retrieve a phylogeny based on a user-defined set of plant species taxonomic names. Branch lengths were estimated for the master plant phylogeny using the branch length adjustment algorithm (BLADJ) in the software Phylocom (Webb, Ackerly & Kembel 2008), which fixes a set of nodes in the tree to specified ages and evenly distributes the ages of the remaining nodes. We used node age estimates from Wikström et al. (2001) as incorporated in the “ages” file in the Phylocom installation. The tree file we used to run the bladj command in Phylocom is provided in multiple formats in Appendix B. See the master plant phylogeny in Appendix B and on Figshare.org. We pruned the master phylogeny for each network. <strong>* Pollinators</strong> For pollinator phylogenies for the unpublished Canadian networks we built a master phylogeny of all animal pollinators across all networks in the study in Mesquite v.2.75 (Maddison & Maddison 2011), based on a variety of published phylogenies. We then pruned the master phylogeny for each network. Pollinator phylogenies from Rezende et al. (2007) were built using a variety of sources (see Rezende et al. 2007 for details). No information on branch lengths was available for pollinator phylogenies, so we assumed all branch lengths equaled one time unit. See the master plant phylogeny in Appendix B and on Figshare.org.
DOI: 10.6084/m9.figshare.1015757
title: Unique Identification of research resources in studies in Reproducibility Project: Cancer Biology

description: Reproducibility Project: Cancer Biology (https://osf.io/e81xl/wiki/home/) aims to reproduce the key experiments from 50 landmark papers in cancer research. As a follow up to the previously published study, which showed a lack of indentifiability of research resources in the published biomedical literature (Vasilevsky, et al. 2014, PeerJ 1:e148), we analyzed 6 resource types reported in these papers to determine the identifiability of these resources. The resource types included antibodies, cell lines, constructs, knockdown reagents, model organisms and software. The results showed an average 85% of the resources were identifiable, and the ability to identify the resources varied amongst the resource types.
DOI: 10.6084/m9.figshare.1015718
title: Interaction Between EPTAC-Modified Gelatin and Surfactants: Surface Tension and Conductivity Methods

description: Gelatin, one of the most valuable macromolecules and by-products of the leather industry, was modified by the addition of 2,3-epoxypropyl trimethyl ammonium chloride (EPTAC). The interaction between EPTAC-modified gelatin (EPTAC-gelatin) and cetyltrimethyl ammonium bromide (CTAB) or sodium dodecyl benzene sulfonate (SDBS) was studied by surface tension and conductivity methods. We found that EPTAC-gelatin adsorbed more CTAB than SDBS but the surface-tension-reducing capabilities of EPTAC-gelatin–CTAB and EPTAC-gelatin–SDBS were almost equal. The micellization process of CTAB was enthalpy-driven but that of SDBS was entropy-driven at low concentrations of EPTAC-gelatin and enthalpy-driven at high concentrations. Based on the analysis of EPTAC-gelatin–CTAB (SDBS) solution properties, interaction models of EPTAC-gelatin–CTAB (SDBS) were proposed.
DOI: 10.6084/m9.figshare.1015757.v2
title: Unique Identification of research resources in studies in Reproducibility Project: Cancer Biology

description: Reproducibility Project: Cancer Biology (https://osf.io/e81xl/wiki/home/) aims to reproduce the key experiments from 50 landmark papers in cancer research. As a follow up to the previously published study, which showed a lack of indentifiability of research resources in the published biomedical literature (Vasilevsky, et al. 2014, PeerJ 1:e148), we analyzed 6 resource types reported in these papers to determine the identifiability of these resources. The resource types included antibodies, cell lines, constructs, knockdown reagents, model organisms and software. The results showed an average 85% of the resources were identifiable, and the ability to identify the resources varied amongst the resource types.
DOI: 10.6084/m9.figshare.1015757.v1
title: Unique Identifcation of research resources in studies in Reproducibility Project: Cancer Biology

description: Reproducibility Project: Cancer Biology (https://osf.io/e81xl/wiki/home/) aims to reproduce the key experiments from 50 landmark papers in cancer research. As a follow up to the previously published study, which showed a lack of indentifiability of research resources in the published biomedical literature (Vasilevsky, et al. 2014, PeerJ 1:e148), we analyzed 6 resource types reported in these papers to determine the identifiability of these resources. The resource types included antibodies, cell lines, constructs, knockdown reagents, model organisms and software. The results showed an average 85% of the resources were identifiable, and the ability to identify the resources varied amongst the resource types.
DOI: 10.6084/m9.figshare.1015718.v3
title: Interaction Between EPTAC-Modified Gelatin and Surfactants: Surface Tension and Conductivity Methods

description: Gelatin, one of the most valuable macromolecules and by-products of the leather industry, was modified by the addition of 2,3-epoxypropyl trimethyl ammonium chloride (EPTAC). The interaction between EPTAC-modified gelatin (EPTAC-gelatin) and cetyltrimethyl ammonium bromide (CTAB) or sodium dodecyl benzene sulfonate (SDBS) was studied by surface tension and conductivity methods. We found that EPTAC-gelatin adsorbed more CTAB than SDBS but the surface-tension-reducing capabilities of EPTAC-gelatin–CTAB and EPTAC-gelatin–SDBS were almost equal. The micellization process of CTAB was enthalpy-driven but that of SDBS was entropy-driven at low concentrations of EPTAC-gelatin and enthalpy-driven at high concentrations. Based on the analysis of EPTAC-gelatin–CTAB (SDBS) solution properties, interaction models of EPTAC-gelatin–CTAB (SDBS) were proposed.
DOI: 10.6084/m9.figshare.1015702
title: SBML model of a synthetic bacterium

description: SBML whole transcription model of a synthetic organism behaving similarly to <em>E. coli</em>. For the methodology to design the model please read http://www.pnas.org/content/109/38/15277.long You could also check the corresponding Genbank annotated sequence for the whole genome at <br>http://dx.doi.org/10.6084/m9.figshare.1015701 For the methodology to create the sequence please read http://www.biomedcentral.com/1752-0509/7/108
DOI: 10.6084/m9.figshare.1015718.v2
title: Interaction Between EPTAC-Modified Gelatin and Surfactants: Surface Tension and Conductivity Methods

description: Gelatin, one of the most valuable macromolecules and by-products of the leather industry, was modified by the addition of 2,3-epoxypropyl trimethyl ammonium chloride (EPTAC). The interaction between EPTAC-modified gelatin (EPTAC-gelatin) and cetyltrimethyl ammonium bromide (CTAB) or sodium dodecyl benzene sulfonate (SDBS) was studied by surface tension and conductivity methods. We found that EPTAC-gelatin adsorbed more CTAB than SDBS but the surface-tension-reducing capabilities of EPTAC-gelatin–CTAB and EPTAC-gelatin–SDBS were almost equal. The micellization process of CTAB was enthalpy-driven but that of SDBS was entropy-driven at low concentrations of EPTAC-gelatin and enthalpy-driven at high concentrations. Based on the analysis of EPTAC-gelatin–CTAB (SDBS) solution properties, interaction models of EPTAC-gelatin–CTAB (SDBS) were proposed.
DOI: 10.6084/m9.figshare.1015701
title: Computationally designed bacterial genome

description: Genbank file of a 4.7 M bs computationally designed bacterial genome. We reshlufled E. coli's genome. This is not expected to work experimentally, but <strong>it is meant to open the discussion on the computational challenges we have to face to design from scratch the whole sequence of a bacterial genome</strong>. For instance, we had to do educated guesses for promoter, terminator and RBS designs. Or for overlapping operons. You could also check its corresponding SBML model of its global transcriptional network. This file has been tested by uploading it to CLC Sequence Viewer 5.1.2. Please cite the original publication http://www.biomedcentral.com/1752-0509/7/108
DOI: 10.6084/m9.figshare.1015673
title: Multiple-stressor effects and ecosystem multifunctionality

description: All individual functions from the 6 published experiments used to calculate the multifunctionality indices.
DOI: 10.6084/m9.figshare.1015674
title: Gaussian Job Archive for C42H66N4O9Zn2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1015675
title: Gaussian Job Archive for C42H66N4O9Zn2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1015701.v1
title: Computationally designed bacterial genome

description: Genbank file of a 4.7 M bs computationally designed bacterial genome. We reshlufled E. coli's genome. This is not expected to work experimentally, but <strong>it is meant to open the discussion on the computational challenges we have to face to design from scratch the whole sequence of a bacterial genome</strong>. For instance, we had to do educated guesses for promoter, terminator and RBS designs. Or for overlapping operons. You could also check its corresponding SBML model of its global transcriptional network. This file has been tested by uploading it to CLC Sequence Viewer 5.1.2. Please cite the original publication http://www.biomedcentral.com/1752-0509/7/108
DOI: 10.6084/m9.figshare.1015675.v1
title: Gaussian Job Archive for C42H66N4O9Zn2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1015674.v1
title: Gaussian Job Archive for C42H66N4O9Zn2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1015671
title: Effects of Human Activities on the World's Most Vulnerable Coral Reefs: Comoros Case Study

description: Effective management of highly biodiverse and threatened reefs requires the identification of human activities driving declines on the particular reef to be managed. The island nation of the Comoros is a model setting to investigate effects of human activities on diverse and threatened coral reefs, with abundant and diverse marine life, local dependence on reef resources, and a variety of anthropogenic pressures on reefs rendering the nation vulnerable to coral reef degradation. Using data from 21 sites throughout the Comoros, we evaluated the relative influence of human activities and other natural and anthropogenic factors on benthic cover and fish richness, abundance, and biomass with the goal of providing prioritized management targets. Human activities including fishing, beach sand extraction, and beachfront housing and development had the strongest relationship with degraded reefs but with some seasonal fluctuation, while geographic patterns most consistently predicted reef degradation across seasons. Comparing analyses conducted with and without human activities as predictors, the inclusion of human activities greatly improved explanatory power. Baseline data on reef biotic composition and localized anthropogenic impacts, monitoring over time, and controlled experiments can facilitate an adaptive management approach for protecting fragile reef ecosystems in the Comoros and elsewhere.
DOI: 10.6084/m9.figshare.1015645
title: Odor-color patterns for USA participants

description: These data represent patterns of colors chosen by participants as congruent or incongruent with an odor. Each row is the color-pattern for one of the 14 odors presented. The columns represent one of the 36 colors that was either chosen as incongruent (1-36) or congruent (37-72) The value in each cell is the total number of times this color was selected. Please refer to the manuscript for details on the odors and colors.
DOI: 10.6084/m9.figshare.1015644
title: Odor-color patterns for Malaysian Chinese participants

description: These data represent patterns of colors chosen by participants as congruent or incongruent with an odor. Each row is the color-pattern for one of the 14 odors presented. The columns represent one of the 36 colors that was either chosen as incongruent (1-36) or congruent (37-72) The value in each cell is the total number of times this color was selected. Please refer to the manuscript for details on the odors and colors.
DOI: 10.6084/m9.figshare.1015645.v1
title: Odor-color patterns for USA participants

description: These data represent patterns of colors chosen by participants as congruent or incongruent with an odor. Each row is the color-pattern for one of the 14 odors presented. The columns represent one of the 36 colors that was either chosen as incongruent (1-36) or congruent (37-72) The value in each cell is the total number of times this color was selected. Please refer to the manuscript for details on the odors and colors.
DOI: 10.6084/m9.figshare.1015671.v1
title: Effects of Human Activities on the World's Most Vulnerable Coral Reefs: Comoros Case Study

description: Effective management of highly biodiverse and threatened reefs requires the identification of human activities driving declines on the particular reef to be managed. The island nation of the Comoros is a model setting to investigate effects of human activities on diverse and threatened coral reefs, with abundant and diverse marine life, local dependence on reef resources, and a variety of anthropogenic pressures on reefs rendering the nation vulnerable to coral reef degradation. Using data from 21 sites throughout the Comoros, we evaluated the relative influence of human activities and other natural and anthropogenic factors on benthic cover and fish richness, abundance, and biomass with the goal of providing prioritized management targets. Human activities including fishing, beach sand extraction, and beachfront housing and development had the strongest relationship with degraded reefs but with some seasonal fluctuation, while geographic patterns most consistently predicted reef degradation across seasons. Comparing analyses conducted with and without human activities as predictors, the inclusion of human activities greatly improved explanatory power. Baseline data on reef biotic composition and localized anthropogenic impacts, monitoring over time, and controlled experiments can facilitate an adaptive management approach for protecting fragile reef ecosystems in the Comoros and elsewhere.
DOI: 10.6084/m9.figshare.1015643
title: Odor-color patterns for Malay participants

description: These data represent patterns of colors chosen by participants as congruent or incongruent with an odor. Each row is the color-pattern for one of the 14 odors presented. The columns represent one of the 36 colors that was either chosen as incongruent (1-36) or congruent (37-72) The value in each cell is the total number of times this color was selected. Please refer to the manuscript for details on the odors and colors.
DOI: 10.6084/m9.figshare.1015644.v1
title: Odor-color patterns for Malaysian Chinese participants

description: These data represent patterns of colors chosen by participants as congruent or incongruent with an odor. Each row is the color-pattern for one of the 14 odors presented. The columns represent one of the 36 colors that was either chosen as incongruent (1-36) or congruent (37-72) The value in each cell is the total number of times this color was selected. Please refer to the manuscript for details on the odors and colors.
DOI: 10.6084/m9.figshare.1015671.v3
title: Effects of Human Activities on the World's Most Vulnerable Coral Reefs: Comoros Case Study

description: Effective management of highly biodiverse and threatened reefs requires the identification of human activities driving declines on the particular reef to be managed. The island nation of the Comoros is a model setting to investigate effects of human activities on diverse and threatened coral reefs, with abundant and diverse marine life, local dependence on reef resources, and a variety of anthropogenic pressures on reefs rendering the nation vulnerable to coral reef degradation. Using data from 21 sites throughout the Comoros, we evaluated the relative influence of human activities and other natural and anthropogenic factors on benthic cover and fish richness, abundance, and biomass with the goal of providing prioritized management targets. Human activities including fishing, beach sand extraction, and beachfront housing and development had the strongest relationship with degraded reefs but with some seasonal fluctuation, while geographic patterns most consistently predicted reef degradation across seasons. Comparing analyses conducted with and without human activities as predictors, the inclusion of human activities greatly improved explanatory power. Baseline data on reef biotic composition and localized anthropogenic impacts, monitoring over time, and controlled experiments can facilitate an adaptive management approach for protecting fragile reef ecosystems in the Comoros and elsewhere.
DOI: 10.6084/m9.figshare.1015641
title: Odor-color patterns for the Netherlands-Residing Chinese participants

description: These data represent patterns of colors chosen by participants as congruent or incongruent with an odor. Each row is the color-pattern for one of the 14 odors presented. The columns represent one of the 36 colors that was either chosen as incongruent (1-36) or congruent (37-72) The value in each cell is the total number of times this color was selected. Please refer to the manuscript for details on the odors and colors.
DOI: 10.6084/m9.figshare.1015642
title: Odor-color patterns for the German participants

description: These data represent patterns of colors chosen by participants as congruent or incongruent with an odor. Each row is the color-pattern for one of the 14 odors presented. The columns represent one of the 36 colors that was either chosen as incongruent (1-36) or congruent (37-72) The value in each cell is the total number of times this color was selected. Please refer to the manuscript for details on the odors and colors.
DOI: 10.6084/m9.figshare.1015643.v2
title: Odor-color patterns for Malay participants

description: These data represent patterns of colors chosen by participants as congruent or incongruent with an odor. Each row is the color-pattern for one of the 14 odors presented. The columns represent one of the 36 colors that was either chosen as incongruent (1-36) or congruent (37-72) The value in each cell is the total number of times this color was selected. Please refer to the manuscript for details on the odors and colors.
DOI: 10.6084/m9.figshare.1015642.v1
title: Odor-color patterns for the German participants

description: These data represent patterns of colors chosen by participants as congruent or incongruent with an odor. Each row is the color-pattern for one of the 14 odors presented. The columns represent one of the 36 colors that was either chosen as incongruent (1-36) or congruent (37-72) The value in each cell is the total number of times this color was selected. Please refer to the manuscript for details on the odors and colors.
DOI: 10.6084/m9.figshare.1015671.v2
title: Effects of Human Activities on the World's Most Vulnerable Coral Reefs: Comoros Case Study

description: Effective management of highly biodiverse and threatened reefs requires the identification of human activities driving declines on the particular reef to be managed. The island nation of the Comoros is a model setting to investigate effects of human activities on diverse and threatened coral reefs, with abundant and diverse marine life, local dependence on reef resources, and a variety of anthropogenic pressures on reefs rendering the nation vulnerable to coral reef degradation. Using data from 21 sites throughout the Comoros, we evaluated the relative influence of human activities and other natural and anthropogenic factors on benthic cover and fish richness, abundance, and biomass with the goal of providing prioritized management targets. Human activities including fishing, beach sand extraction, and beachfront housing and development had the strongest relationship with degraded reefs but with some seasonal fluctuation, while geographic patterns most consistently predicted reef degradation across seasons. Comparing analyses conducted with and without human activities as predictors, the inclusion of human activities greatly improved explanatory power. Baseline data on reef biotic composition and localized anthropogenic impacts, monitoring over time, and controlled experiments can facilitate an adaptive management approach for protecting fragile reef ecosystems in the Comoros and elsewhere.
DOI: 10.6084/m9.figshare.1015640
title: Odor-color patterns for the Dutch participants

description: These data represent patterns of colors chosen by participants as congruent or incongruent with an odor. Each row is the color-pattern for one of the 14 odors presented. The columns represent one of the 36 colors that was either chosen as incongruent (1-36) or congruent (37-72) The value in each cell is the total number of times this color was selected. Please refer to the manuscript for details on the odors and colors.