cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5120020.v1
title: Comparative genomic survey of Bacillus cereus isolates in the Brazilian dairy production chain

description: Assembled genomes of 69 <i>Bacillus cereus</i> isolates from various points and locations of the dairy production process in Brazil. <br>Contig files labelled by BIGs IDs, which are included with isolate info spreadsheet.
DOI: 10.6084/m9.figshare.5119966
title: Dataset: Dynamics of neural representations when searching for exemplars and categories of human and non-human faces

description: Supporting data for:Dynamics of neural representations when searching for exemplars and categories of human and non-human facesBayet L., Zinszer B., Pruitt Z., Aslin R. N., & Wu R. (2018) Scientific Reports doi: 10.1038/s41598-018-31526-y<br>See also:Wu, R. et al. Rapid attentional selection of non-native stimuli despite perceptual narrowing. J. Cogn. Neurosci. 27, 2299–2307 (2015).<br><br>
DOI: 10.6084/m9.figshare.5119981
title: Data and analysis for Experiment 2

description: Data and analysis for Experiment 2 (balance contrast) from "Persistent biases in binocular rivalry dynamics within the visual field"<br>
DOI: 10.6084/m9.figshare.5119981.v1
title: Data and analysis for Experiment 2

description: Data and analysis for Experiment 2 (balance contrast) from "Persistent biases in binocular rivalry dynamics within the visual field"<br>
DOI: 10.6084/m9.figshare.5120005.v1
title: Plant diversity changes associated to Gunnera tinctoria invasion in Irish grasslands

description: In this study we have assessed and quantify the impacts of the invasive species <i>Gunnera tinctoria</i> on vegetation biodiversity at three different habitats, namely grasslands, riparian and coastal cliffs. Habitat selection was based on the extent and dominance of <i>G. tinctoria</i> invasion, e.g. grasslands and riparian habitats. Coastal cliffs were chosen as they are one of the few habitats which have little to no human influences. We hypothesis that alpha and beta vegetation diversity will be significantly reduced at all habitat types, irrespective if the habitats are highly disturbed, human influenced or semi-natural. Additionally, we hypothesized that changes in plant assemblage structure and composition will be associated to the invasion of <i>G. tinctoria</i>.Plant assemblages were sampled in July 2009 at twelve sites in three different habitats (grassland, coastal cliff and waterways), differing in the invasion status by the <i>Gunnera tinctoria</i>, in Achill Island, Co. Mayo, West Ireland. Within each habitat two locations were selected and within each location one invaded and one non-invaded site were sampled. The two locations in the grassland habitat were Dooega (53° 57.2’ N, 9°57.9’ W) and Sraheens (53° 57.2’ N, 9°57.9’ W), the two locations in the coastal cliff habitat were Dooega and Keel, and in the waterways the two sampled locations were Ashleam and Dooega River. In each habitat, invaded and non-invaded sites were chosen so that they were geographically interspersed. When possible, sites were chosen randomly from a larger pool of candidate sites and based on monitoring programme in the area. At each site, an area of 100 x 100 m was randomly selected were 4 replicated 1 m<sup>2</sup> quadrats were sampled. Percentage cover was estimated using the point-intercept method with a quadrat of 1 m<sup>2</sup> and 144 intersection points. Most conspicuous taxa were identified to species level, while others were grouped into functional-form groups. The intersection data was then transformed into percentage cover. Plants present in the quadrat not recorded by this method were given a cover of 1%. In the case of multi-strata growth, total percentage cover exceeded 100%.
DOI: 10.6084/m9.figshare.5119870
title: Engle_BLANK.raw

description: Mass spectrometry characterization of post-translational modification of <i>Saccharomyces cerevisiae </i>protein <i>Deg1</i>-Sec62-N153D<br>
DOI: 10.6084/m9.figshare.5120005.v3
title: Plant diversity changes associated to <i>Gunnera tinctoria</i> invasion in Irish grasslands

description: In this study we have assessed and quantify the impacts of the invasive species <i>Gunnera tinctoria</i> on vegetation biodiversity at three different habitats, namely grasslands, riparian and coastal cliffs. Habitat selection was based on the extent and dominance of <i>G. tinctoria</i> invasion, e.g. grasslands and riparian habitats. Coastal cliffs were chosen as they are one of the few habitats which have little to no human influences. We hypothesized that alpha and beta vegetation diversity will be significantly reduced at all habitat types, irrespective if the habitats are highly disturbed, human influenced or semi-natural. Additionally, we hypothesized that changes in plant assemblage structure and composition will be associated to the invasion of <i>G. tinctoria</i>.Plant assemblages were sampled in July 2009 at twelve sites in three different habitats (grassland, coastal cliff and waterways), differing in the invasion status by the <i>Gunnera tinctoria</i>, in Achill Island, Co. Mayo, West Ireland. Within each habitat two locations were selected and within each location one invaded and one non-invaded site were sampled. The two locations in the grassland habitat were Dooega (53° 57.2’ N, 9°57.9’ W) and Sraheens (53° 57.2’ N, 9°57.9’ W), the two locations in the coastal cliff habitat were Dooega and Keel, and in the waterways the two sampled locations were Ashleam and Dooega River. In each habitat, invaded and non-invaded sites were chosen so that they were geographically interspersed. When possible, sites were chosen randomly from a larger pool of candidate sites and based on monitoring programme in the area. At each site, an area of 100 x 100 m was randomly selected were 4 replicated 1 m<sup>2</sup> quadrats were sampled. Percentage cover was estimated using the point-intercept method with a quadrat of 1 m<sup>2</sup> and 144 intersection points. Most conspicuous taxa were identified to species level, while others were grouped into functional-form groups. The intersection data was then transformed into percentage cover. Plants present in the quadrat not recorded by this method were given a cover of 1%. In the case of multi-strata growth, total percentage cover exceeded 100%.
DOI: 10.6084/m9.figshare.5119861
title: Dataset 1 from: Proteins evolve on the edge of supramolecular self-assembly. Garcia-Seisdedos H, Empereur-Mot C, Elad N, Levy ED

description: This file is the supplementary Dataset 1 from:<br>Proteins evolve on the edge of supramolecular self-assembly. Garcia-Seisdedos H, Empereur-Mot C, Elad N, Levy ED<br><br>It contains computed values of nDp (normal distance to the closest bounding plane) for homo-oligomeric structures present in PDB. The tabulated file is organized as follows:<br><br>- code: code of the 'Biological assembly', in the form of xxxx_1, xxx_2. The extensions _1/_2 means that there can be multiple possible assemblies proposed by PDB.<br>- chain: chain identifier<br>- aa: residue name<br>- residue_number: residue number (renumbered from the SEQRES sequence)<br>- No subunits: Number of subunits in the homo-oligomer<br>- Symmetry: Internal symmetry of the homo-oligomer<br>- X: x-coordinate of the residue<br>- Y: y-coordinate of the residue<br>- Z: z-coordinate of the residue<br>- relative ASA: relative accessible surface area of the residue, calculated using AREAIMOL<br>- stickiness: stickiness of the patch surrounding the residue, as defined in Levy et al. PNAS 2012.<br>- d_plan: distance of the residue to the closest bounding plane.<br>- d_plan_symAxis: type of symmetry axis which the bounding plane is associated to (180 = 2-fold; 120 = 3-fold; etc.)<br>- d_plan_face : face-id of the homo-oligomer the axis is associated to<br>- h_100_repre : indicates whether the homo-oligomer is part of a set non-redundant at 100% sequence identity<br>- h_90_repre : indicates whether the homo-oligomer is part of a set non-redundant at 90% sequence identity<br>- h_80_repre : indicates whether the homo-oligomer is part of a set non-redundant at 80% sequence identity<br><br><br>
DOI: 10.6084/m9.figshare.5119870.v1
title: Engle_BLANK.raw

description: Mass spectrometry characterization of post-translational modification of <i>Saccharomyces cerevisiae </i>protein <i>Deg1</i>-Sec62-N153D<br>
DOI: 10.6084/m9.figshare.5119909
title: Data and analysis for Experiment 4

description: Data and analysis code from Experiment 4 in "Persistent biases in rivalry dynamics within the visual field<br>
DOI: 10.6084/m9.figshare.5120005.v2
title: Plant diversity changes associated to <i>Gunnera tinctoria<i> invasion in Irish grasslands</i></i>

description: In this study we have assessed and quantify the impacts of the invasive species <i>Gunnera tinctoria</i> on vegetation biodiversity at three different habitats, namely grasslands, riparian and coastal cliffs. Habitat selection was based on the extent and dominance of <i>G. tinctoria</i> invasion, e.g. grasslands and riparian habitats. Coastal cliffs were chosen as they are one of the few habitats which have little to no human influences. We hypothesis that alpha and beta vegetation diversity will be significantly reduced at all habitat types, irrespective if the habitats are highly disturbed, human influenced or semi-natural. Additionally, we hypothesized that changes in plant assemblage structure and composition will be associated to the invasion of <i>G. tinctoria</i>.Plant assemblages were sampled in July 2009 at twelve sites in three different habitats (grassland, coastal cliff and waterways), differing in the invasion status by the <i>Gunnera tinctoria</i>, in Achill Island, Co. Mayo, West Ireland. Within each habitat two locations were selected and within each location one invaded and one non-invaded site were sampled. The two locations in the grassland habitat were Dooega (53° 57.2’ N, 9°57.9’ W) and Sraheens (53° 57.2’ N, 9°57.9’ W), the two locations in the coastal cliff habitat were Dooega and Keel, and in the waterways the two sampled locations were Ashleam and Dooega River. In each habitat, invaded and non-invaded sites were chosen so that they were geographically interspersed. When possible, sites were chosen randomly from a larger pool of candidate sites and based on monitoring programme in the area. At each site, an area of 100 x 100 m was randomly selected were 4 replicated 1 m<sup>2</sup> quadrats were sampled. Percentage cover was estimated using the point-intercept method with a quadrat of 1 m<sup>2</sup> and 144 intersection points. Most conspicuous taxa were identified to species level, while others were grouped into functional-form groups. The intersection data was then transformed into percentage cover. Plants present in the quadrat not recorded by this method were given a cover of 1%. In the case of multi-strata growth, total percentage cover exceeded 100%.
DOI: 10.6084/m9.figshare.5119765
title: Geophysical, cognitive, and social data for 96 countries

description: This data set will allow the reader to analyze variables used by Federico R. León in the study "Diminished UV Radiation Enhances Country’s Cognitive Ability, Wealth, and Institutions through Health and Education".
DOI: 10.6084/m9.figshare.5119807
title: Bursaria_experiment_data.csv

description: 1 data set containing density time series for Paramecium bursaria in four different treatments1 data set with the results of a foraging experiment with the predatory copepod Eucyclops agilis preying on Paramecium bursaria1 data set with flowcam measurements for individual Paramecium bursaria for the four different treatments considered in the paper.<br>For info on experimental details please check:<br>Gibert et al 2017, The ecological consequences of environmentally inducedphenotypic changes, Ecology Letters
DOI: 10.6084/m9.figshare.5119861.v1
title: Dataset 1 from: Proteins evolve on the edge of supramolecular self-assembly. Garcia-Seisdedos H, Empereur-Mot C, Elad N, Levy ED

description: This file is the supplementary Dataset 1 from:<br>Proteins evolve on the edge of supramolecular self-assembly. Garcia-Seisdedos H, Empereur-Mot C, Elad N, Levy ED<br><br>It contains computed values of nDp (normal distance to the closest bounding plane) for homo-oligomeric structures present in PDB. The tabulated file is organized as follows:<br><br>- code: code of the 'Biological assembly', in the form of xxxx_1, xxx_2. The extensions _1/_2 means that there can be multiple possible assemblies proposed by PDB.<br>- chain: chain identifier<br>- aa: residue name<br>- residue_number: residue number (renumbered from the SEQRES sequence)<br>- No subunits: Number of subunits in the homo-oligomer<br>- Symmetry: Internal symmetry of the homo-oligomer<br>- X: x-coordinate of the residue<br>- Y: y-coordinate of the residue<br>- Z: z-coordinate of the residue<br>- relative ASA: relative accessible surface area of the residue, calculated using AREAIMOL<br>- stickiness: stickiness of the patch surrounding the residue, as defined in Levy et al. PNAS 2012.<br>- d_plan: distance of the residue to the closest bounding plane.<br>- d_plan_symAxis: type of symmetry axis which the bounding plane is associated to (180 = 2-fold; 120 = 3-fold; etc.)<br>- d_plan_face : face-id of the homo-oligomer the axis is associated to<br>- h_100_repre : indicates whether the homo-oligomer is part of a set non-redundant at 100% sequence identity<br>- h_90_repre : indicates whether the homo-oligomer is part of a set non-redundant at 90% sequence identity<br>- h_80_repre : indicates whether the homo-oligomer is part of a set non-redundant at 80% sequence identity<br><br><br>
DOI: 10.6084/m9.figshare.5119909.v1
title: Data and analysis for Experiment 4

description: Data and analysis code from Experiment 4 in "Persistent biases in rivalry dynamics within the visual field<br>
DOI: 10.6084/m9.figshare.5119807.v1
title: Bursaria_experiment_data.csv

description: 1 data set containing density time series for Paramecium bursaria in four different treatments1 data set with the results of a foraging experiment with the predatory copepod Eucyclops agilis preying on Paramecium bursaria1 data set with flowcam measurements for individual Paramecium bursaria for the four different treatments considered in the paper.<br>For info on experimental details please check:<br>Gibert et al 2017, The ecological consequences of environmentally inducedphenotypic changes, Ecology Letters
DOI: 10.6084/m9.figshare.5119756
title: TEAM Models_Mathieu2008.pdf

description: Team models: Mathieu et al. (2008)
DOI: 10.6084/m9.figshare.5119684
title: Effect of changing window type and ventilation strategy on indoor thermal environment of existing garment factories in Bangladesh

description: This paper presents two workable solutions that can significantly improve the indoor thermal environment within workspaces in existing ready-made garment (RMG) factories in the tropical climatic context of Bangladesh. The research involved field studies in three multi-storey factory buildings, interviews with workers and owners and simulation studies. Field data indicated that the existing window configurations and limiting the ventilation strategy to occupied hours caused overheating of the indoor environment. Among a list of proposals, the building owners saw value in implementing two solutions (i.e. altering existing window type to one with a higher effective opening area and adopting a night-time ventilation strategy) in their existing buildings as well as proposed new buildings. To quantify the benefits, a validated simulation study was conducted. The findings confirm that these two interventions can provide reductions of up to 23% in overheated working hours and in so doing, improve workers’ thermal comfort and well-being.
DOI: 10.6084/m9.figshare.5119759
title: Loffreda, Jacchetti et al., 2017 - Dataset

description: Data used to generate the plots of the manuscript "Live-cell p53 single molecule binding is modulated by C-terminal acetylation and correlates with transcriptional activity" by Loffreda, Jacchetti et al., 2017.<b></b>
DOI: 10.6084/m9.figshare.5119684.v1
title: Effect of changing window type and ventilation strategy on indoor thermal environment of existing garment factories in Bangladesh

description: This paper presents two workable solutions that can significantly improve the indoor thermal environment within workspaces in existing ready-made garment (RMG) factories in the tropical climatic context of Bangladesh. The research involved field studies in three multi-storey factory buildings, interviews with workers and owners and simulation studies. Field data indicated that the existing window configurations and limiting the ventilation strategy to occupied hours caused overheating of the indoor environment. Among a list of proposals, the building owners saw value in implementing two solutions (i.e. altering existing window type to one with a higher effective opening area and adopting a night-time ventilation strategy) in their existing buildings as well as proposed new buildings. To quantify the benefits, a validated simulation study was conducted. The findings confirm that these two interventions can provide reductions of up to 23% in overheated working hours and in so doing, improve workers’ thermal comfort and well-being.
DOI: 10.6084/m9.figshare.5117857
title: Introducing alternative and web base metrics to publications planners at ISMPP annual meeting 2017

description: Presentation at ISMPP 2017 introducing altmetrics to publications planners at the annual meeting. Co-presenters: Steve Rizk (Genentech) and Paul Lane (Envision Pharma Group)
DOI: 10.6084/m9.figshare.5117827
title: GenomeSize_lowcoverage_Maizedata

description: Maize landrace data
DOI: 10.6084/m9.figshare.5117827.v1
title: GenomeSize_lowcoverage_Maizedata

description: Maize landrace data
DOI: 10.6084/m9.figshare.5117839
title: Enzyme activities and bacterial cell counts

description: Peptidase activity was measured using L-Leucine-4-Methylcoumarin-7-amide hydrochloride as substrate proxy (final substrate concentration: 350 uM). Bacterial cells were counted using flow cytometry. <br>
DOI: 10.6084/m9.figshare.5117839.v1
title: Enzyme activities and bacterial cell counts

description: Peptidase activity was measured using L-Leucine-4-Methylcoumarin-7-amide hydrochloride as substrate proxy (final substrate concentration: 350 uM). Bacterial cells were counted using flow cytometry. <br>
DOI: 10.6084/m9.figshare.5117806
title: Supplementary 8 from Mice as stowaways? Colonization history of Danish striped field mice

description: Species from the steppe region of Eastern Europe likely colonized Northwestern Europe in connection with agriculture after 6500 BP. The striped field mouse (<i>Apodemus agrarius</i> Pallas, 1783), is a steppe-derived species often found in human crops, that is common on the southern Danish islands of Lolland and Falster, which have been isolated from mainland Europe because approximately10 300–8000 BP. Thus, this species could have been brought in with humans in connection with agriculture, or it could be an earlier natural invader. We sequenced 86 full mitochondrial genomes from the Northwestern range of the striped field mouse, analysed phylogenetic relationships and estimated divergence time. The results supported human-induced colonization of Denmark in the Subatlantic or Subboreal period. A newly discovered population from Central Jutland in Denmark diverged from Falster approximately 100–670 years ago, again favouring human introduction. One individual from Sweden turned out to be a recent introduction from Central Jutland.
DOI: 10.6084/m9.figshare.5117857.v1
title: Introducing alternative and web base metrics to publications planners at ISMPP annual meeting 2017

description: Presentation at ISMPP 2017 introducing altmetrics to publications planners at the annual meeting. Co-presenters: Steve Rizk (Genentech) and Paul Lane (Envision Pharma Group)
DOI: 10.6084/m9.figshare.5117806.v1
title: Supplementary 8 from Mice as stowaways? Colonization history of Danish striped field mice

description: Species from the steppe region of Eastern Europe likely colonized Northwestern Europe in connection with agriculture after 6500 BP. The striped field mouse (<i>Apodemus agrarius</i> Pallas, 1783), is a steppe-derived species often found in human crops, that is common on the southern Danish islands of Lolland and Falster, which have been isolated from mainland Europe because approximately10 300–8000 BP. Thus, this species could have been brought in with humans in connection with agriculture, or it could be an earlier natural invader. We sequenced 86 full mitochondrial genomes from the Northwestern range of the striped field mouse, analysed phylogenetic relationships and estimated divergence time. The results supported human-induced colonization of Denmark in the Subatlantic or Subboreal period. A newly discovered population from Central Jutland in Denmark diverged from Falster approximately 100–670 years ago, again favouring human introduction. One individual from Sweden turned out to be a recent introduction from Central Jutland.
DOI: 10.6084/m9.figshare.5117800
title: Appendix 1 from Estimating adult sex ratios in nature

description: R code to generate box panel 1: Comparison of ASR measures from raw counts of unmarked male and female individuals with estimates obtained with a detection-based abundance model.
DOI: 10.6084/m9.figshare.5117788
title: Raw data from Ant queens increase their reproductive efforts after pathogen infection

description: Egg laying rates and infection loads of C. obscurior queens
DOI: 10.6084/m9.figshare.5117779
title: Supplementary 2 from Mice as stowaways? Colonization history of Danish striped field mice

description: Species from the steppe region of Eastern Europe likely colonized Northwestern Europe in connection with agriculture after 6500 BP. The striped field mouse (<i>Apodemus agrarius</i> Pallas, 1783), is a steppe-derived species often found in human crops, that is common on the southern Danish islands of Lolland and Falster, which have been isolated from mainland Europe because approximately10 300–8000 BP. Thus, this species could have been brought in with humans in connection with agriculture, or it could be an earlier natural invader. We sequenced 86 full mitochondrial genomes from the Northwestern range of the striped field mouse, analysed phylogenetic relationships and estimated divergence time. The results supported human-induced colonization of Denmark in the Subatlantic or Subboreal period. A newly discovered population from Central Jutland in Denmark diverged from Falster approximately 100–670 years ago, again favouring human introduction. One individual from Sweden turned out to be a recent introduction from Central Jutland.
DOI: 10.6084/m9.figshare.5117782
title: Data and Code from Monte Carlo profile confidence intervals for dynamic systems

description: Data and code to reproduce the results in both the manuscript and the supplementary text. Files are combined in a plain text tar format. A README file describes the contents of each file.