cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20277759.v4
title: Fungal genome size and composition reflect ecological strategies along soil fertility gradientsadd code and derived data

description: This dataset includes all data as well as the scripts used to produce figures from both the main text and the supporting information from Zhang et al. (2023) " Fungal genome size and composition reflect ecological strategies along soil fertility gradients". <br> Detailed description: genome_size_lifestyle.csv: the file containing genome size and lifestyles for all fungi. ncbi_fungi_GC_content.csv: files containing GC content data from NCBI. Fungi_all_gs_gc_match.csv: files containing fungal species that both have the GC and genome size values. genome_size_fungal_traits.csv: files containing other fungal traits data for species that have genome size data. <br> <br> All data above are the raw data files. By contrast, the following data files, including Australian_Microbiome_GC_CWM.csv, Australian_Microbiome_Genomesize_CWM.csv, Appendix_S1.csv, Appendix_S3.csv are derived data and the code Fig3.R can be used to generate these data files. Fig4_slope_data.csv was generated from FigS4_stats.R, FigS5_stats.R, FigS6_stats.R. <br> For each of these figures there is their respective R script and the reorganized dataset used to produce them. R scripts are responsible for the production of Figures 1-4 in the main text and most of the supplement respectively.
DOI: 10.5281/zenodo.6803362
title: Data, code and software to reproduce the article entitled "Modeling soil-plant functioning of intercrops using comprehensive and generic formalisms implemented in the STICS model"

description: This is the data, code and software to reproduce the article entitled " Modeling soil-plant functioning of intercrops using comprehensive and generic formalisms implemented in the STICS model". Here is a summary of the paper: The growing demand for sustainable agriculture is raising interest in intercropping for its multiple potential benefits to avoid or limit the use of chemical inputs or increase the production per surface unit. Predicting the existence and magnitude of those benefits remains a challenge given the numerous interactions between interspecific plant-plant relationships, their environment and the agricultural practices. Soil-crop models are critical in understanding these interactions in dynamics during the whole growing season, but few models are capable of accurately simulating intercropping systems. In this study, we propose a set of simple and generic formalisms for simulating key interactions in intercropping systems that can be readily included into existing dynamic crop models. This requires simulating important processes such as development, light interception, plant growth, N and water balance, and yield formation in response to management practices, soil conditions, and climate. These formalisms were integrated into the STICS soil-crop model and evaluated using observed data of intercropping systems of cereal and legumes mixtures, including Faba bean-Wheat, Pea-Barley, Sunflower-Soybean, and Wheat-Pea mixtures. We demonstrate that the proposed formalisms provide a comprehensive simulation of soil-plant interactions in various types of bispecific intercrops. The model was found consistent and generic under a range of spring and winter intercrops (nRMSE = 25% for maximum leaf area index, 23% for shoot biomass at harvest, and 18% for yield). This is the first time a complete set of formalisms has been developed and published for simulating intercropping systems and integrated into a soil-crop model. With its emphasis on being generic, sufficiently accurate, simple, and easy to parameterize, STICS is well-suited to help researchers designing <em>in silico</em> the agroecological transition by virtually pre-screening sustainable, manageable intercrop systems adapted to local conditions.
DOI: 10.5281/zenodo.7712791
title: Data, code and software to reproduce the article entitled "Modeling soil-plant functioning of intercrops using comprehensive and generic formalisms implemented in the STICS model"

description: This is the data, code and software to reproduce the article entitled " Modeling soil-plant functioning of intercrops using comprehensive and generic formalisms implemented in the STICS model". Here is a summary of the paper: The growing demand for sustainable agriculture is raising interest in intercropping for its multiple potential benefits to avoid or limit the use of chemical inputs or increase the production per surface unit. Predicting the existence and magnitude of those benefits remains a challenge given the numerous interactions between interspecific plant-plant relationships, their environment and the agricultural practices. Soil-crop models are critical in understanding these interactions in dynamics during the whole growing season, but few models are capable of accurately simulating intercropping systems. In this study, we propose a set of simple and generic formalisms for simulating key interactions in intercropping systems that can be readily included into existing dynamic crop models. This requires simulating important processes such as development, light interception, plant growth, N and water balance, and yield formation in response to management practices, soil conditions, and climate. These formalisms were integrated into the STICS soil-crop model and evaluated using observed data of intercropping systems of cereal and legumes mixtures, including Faba bean-Wheat, Pea-Barley, Sunflower-Soybean, and Wheat-Pea mixtures. We demonstrate that the proposed formalisms provide a comprehensive simulation of soil-plant interactions in various types of bispecific intercrops. The model was found consistent and generic under a range of spring and winter intercrops (nRMSE = 25% for maximum leaf area index, 23% for shoot biomass at harvest, and 18% for yield). This is the first time a complete set of formalisms has been developed and published for simulating intercropping systems and integrated into a soil-crop model. With its emphasis on being generic, sufficiently accurate, simple, and easy to parameterize, STICS is well-suited to help researchers designing <em>in silico</em> the agroecological transition by virtually pre-screening sustainable, manageable intercrop systems adapted to local conditions.
DOI: 10.6084/m9.figshare.20277759.v3
title: Fungal genome size and composition reflect ecological strategies along soil fertility gradientsadd code and derived data

description: This dataset includes all data as well as the scripts used to produce figures from both the main text and the supporting information from Zhang et al. (2023) " Fungal genome size and composition reflect ecological strategies along soil fertility gradients". <br> <br> Detailed description: genome_size_lifestyle.csv: the file containing genome size and lifestyles for all fungi. ncbi_fungi_GC_content.csv: files containing GC content data from NCBI. Fungi_all_gs_gc_match.csv: files containing fungal species that both have the GC and genome size values. genome_size_fungal_traits.csv: files containing other fungal traits data for species that have genome size data. <br> <br> All data above are the raw data files. By contrast, the following data files, including Australian_Microbiome_GC_CWM.csv, Australian_Microbiome_Genomesize_CWM.csv, Appendix_S1.csv, Appendix_S3.csv are derived data and the code Fig3.R can be used to generate these data files. <br> <br> For each of these figures there is their respective R script and the reorganized dataset used to produce them. R scripts are responsible for the production of Figures 1-3 in the main text and most of the supplement respectively. Fig 4 in the main text was produced once slopes were generated from code FigS4.R, FigS5_stats.R, and FigS6_stats.R.
DOI: 10.6073/pasta/f959751ce226c9b0617935a43d9d4c48
title: Songbird yields resulting from different forest management practices in the Oregon Coast Range, 2019-2021

description: Data in this package was used to model the responses of forest songbirds to landscape scale forest management strategies. The majority of data was derived from emprical studies (avian point counts) conducted by the principal investigator or mined from the literature. Gaps in the data were filled in via expert opinion, considering the life history and habitat needs of the species.
DOI: 10.6084/m9.figshare.22241527
title: VCaP_ATAC_ENZ3w_0nM_rep2

description: VCaP_ATAC_ENZ3w_0nM_rep2
DOI: 10.6084/m9.figshare.22241527.v1
title: VCaP_ATAC_ENZ3w_0nM_rep2

description: VCaP_ATAC_ENZ3w_0nM_rep2
DOI: 10.6084/m9.figshare.22241533
title: VCaP_ATAC_ENZ3w_1nM-DHT_rep1

description: VCaP_ATAC_ENZ3w_1nM-DHT_rep1
DOI: 10.6084/m9.figshare.22241533.v1
title: VCaP_ATAC_ENZ3w_1nM-DHT_rep1

description: VCaP_ATAC_ENZ3w_1nM-DHT_rep1
DOI: 10.5281/zenodo.7712811
title: Perceived safety and attractiveness of city streets in Frankfurt, Germany: ratings and explanations

description: How safe or attractive do different people perceive streets to be and why? In this repository we share the data we collected and analysed for the paper "Is it safe to be attractive? Disentangling the influence of streetscape features on the perceived safety and attractiveness of city streets". The data contain ratings of perceived safety and attractiveness (using a 5-point Likert scale) coming from 403 participants who were asked to virtually navigate city streets in Frankfurt, Germany, through a sequence of street-level images. Moreover it contains their explanations of the ratings (in their own words). In total we have collected data for 753 locations. In particular: 7989 rating pairs of perceived safety and attractiveness 19114 keywords used to explain the safety ratings 18232 keywords used to explain the attractiveness ratings
DOI: 10.5281/zenodo.7712810
title: Perceived safety and attractiveness of city streets in Frankfurt, Germany: ratings and explanations

description: How safe or attractive do different people perceive streets to be and why? In this repository we share the data we collected and analysed for the paper "Is it safe to be attractive? Disentangling the influence of streetscape features on the perceived safety and attractiveness of city streets". The data contain ratings of perceived safety and attractiveness (using a 5-point Likert scale) coming from 403 participants who were asked to virtually navigate city streets in Frankfurt, Germany, through a sequence of street-level images. Moreover it contains their explanations of the ratings (in their own words). In total we have collected data for 753 locations. In particular: 7989 rating pairs of perceived safety and attractiveness 19114 keywords used to explain the safety ratings 18232 keywords used to explain the attractiveness ratings
DOI: 10.6084/m9.figshare.22241539
title: VCaP_ATAC_ENZ3w_1nM-DHT_rep2

description: VCaP_ATAC_ENZ3w_1nM-DHT_rep2
DOI: 10.6084/m9.figshare.22241539.v1
title: VCaP_ATAC_ENZ3w_1nM-DHT_rep2

description: VCaP_ATAC_ENZ3w_1nM-DHT_rep2
DOI: 10.15151/esrf-es-998388450
title: Unravelling structure-properties relationship of bio-compatible cements during setting

description: We aim at monitoring in situ and simultaneously the evolution of mechanical properties and of phase composition of several hydraulic binders, such as cements for bone reconstruction, during their setting. These materials experience a liquid-to-solid transition due to the dissolution of a reactive powder and the reprecipitation of more stable products. This class of materials has a huge technological and economical impact on our societies, mainly because of this setting process. Beyond construction industry, it allows to use bone cement in mini-invasive surgery techniques or to 3D-print implants that harden as soon as printed. Understanding the link between the evolution of rheological properties of the printed paste and the extent of its chemical reaction is therefore a key point. The results will thus bring critical information to understand the structure-properties relationship during the solidification, serving to refine cements formulation in various fields of engineering.
DOI: 10.14469/hpc/11294
title: TS3 for C-O break IRC

description: Gaussian 16 (C01) calculation
DOI: 10.14469/hpc/11307
title: Removal of OMe from B(OMe)3 by acetic acid, TS1, G = -827.764488, IRC

description: Gaussian 16 (C01) calculation
DOI: 10.14469/hpc/11309
title: TS3 for C-O break, rotamer5, G = -807.880172

description: Gaussian 16 (C01) calculation
DOI: 10.14469/hpc/11323
title: TS3 for C-O break, rotamer5, G = -807.880172, IRC

description: Gaussian 16 (C01) calculation
DOI: 10.14469/hpc/11340
title: Start point 3 for C-O break, Def2-TZVPP, conformer 1, G = -808.917515

description: Gaussian 16 (C01) calculation
DOI: 10.14469/hpc/11353
title: TS3 C-O break, rotamer6, Def2-SVPP, G = -807.882963, DG = 24.3

description: Gaussian 16 (C01) calculation
DOI: 10.14469/hpc/11295
title: Start point 3 for C-O break, Def2-SVPP, G = -807.915918

description: Gaussian 16 (C01) calculation
DOI: 10.14469/hpc/11313
title: TS3 for C-O break, rotamer4, G = -807.866492

description: Gaussian 16 (C01) calculation
DOI: 10.14469/hpc/11316
title: TS3 for C-O break, rotamer3, Def2-TZVPP, G = -808.877693, DG = 25.0

description: Gaussian 16 (C01) calculation
DOI: 10.14469/hpc/11326
title: Start point 3 for C-O break, G = -807.921627

description: Gaussian 16 (C01) calculation
DOI: 10.14469/hpc/11292
title: TS4 from alex for C-O break, Def2-TZVPP, G = -808.867879

description: Gaussian 16 (C01) calculation
DOI: 10.14469/hpc/11296
title: Removal of OMe from B(OMe)3 by acetic acid, G = -827.764488

description: Gaussian 16 (C01) calculation
DOI: 10.14469/hpc/11314
title: TS3 for C-O break, rotamer3, G = -807.880192, IRC

description: Gaussian 16 (C01) calculation
DOI: 10.14469/hpc/11315
title: Removal of OMe from B(OMe)3 by acetic acid, G = -827.764488, =&gt; Displacement of MeOH by MeNH2, G = -923.494767

description: Gaussian 16 (C01) calculation
DOI: 10.14469/hpc/11365
title: Regeneration, =&gt; Displacement of HOH by MeNH2, TS, G = -884.240285

description: Gaussian 16 (C01) calculation
DOI: 10.14469/hpc/11293
title: Start point from alex for C-O break, Def2-TZVPP, G = -808.911577

description: Gaussian 16 (C01) calculation
DOI: 10.14469/hpc/11304
title: TS3 for C-O break, rotamer3, G = -807.880192

description: Gaussian 16 (C01) calculation
DOI: 10.14469/hpc/11305
title: Removal of H2O, catalyst regeneration step, Def2-TZVPP, G = -789.488437

description: Gaussian 16 (C01) calculation
DOI: 10.14469/hpc/11321
title: TS3 for C-O break, rotamer5, Def2-TZVPP, G= -808.877574, DG = 25.1

description: Gaussian 16 (C01) calculation
DOI: 10.14469/hpc/11385
title: TS3 for C-O break, rotamer6, Def2-SVPP, G = -807.882963, DG = 24.3 =&gt; 27.4 with Water solvating the sp2-O TS, G = -884.227490 IRC

description: Gaussian 16 (C01) calculation
DOI: 10.14469/hpc/11290
title: TS3 for C-O break, G = -807.867362

description: Gaussian 16 (C01) calculation
DOI: 10.14469/hpc/11310
title: TS3 for C-O break, rotamer2, G = -807.866490

description: Gaussian 16 (C01) calculation
DOI: 10.14469/hpc/11366
title: Regeneration, =&gt; Displacement of HOH by MeNH2, TS4, IRC

description: Gaussian 16 (C01) calculation
DOI: 10.14469/hpc/11384
title: TS3 for C-O break, G = -807.921627 + 1 H2O solvating carbonyl, G = -884.271089

description: Gaussian 16 (C01) calculation
DOI: 10.14469/hpc/11312
title: Removal of H2O, catalyst regeneration step, TS5, + MeNH2 to displace water and regenerate start point G = -884.246745

description: Gaussian 16 (C01) calculation
DOI: 10.14469/hpc/11320
title: Removal of H2O, catalyst regeneration step, + MeNH2 to displace water and regenerate start point, TS5, G = -884.246745, IRC

description: Gaussian 16 (C01) calculation
DOI: 10.14469/hpc/11364
title: Removal of OMe from B(OMe)3 by acetic acid, =&gt; Displacement of MeOH by MeNH2, TS2, G = -923.491815

description: Gaussian 16 (C01) calculation
DOI: 10.14469/hpc/11382
title: TS3 for C-O break, rotamer6, Def2-SVPP, G = -807.882963, DG = 24.3 =&gt; + Water solvating the sp2-O TS, G = -884.227490

description: Gaussian 16 (C01) calculation
DOI: 10.14469/hpc/11291
title: TS3 for C-O break, rotamer1, G = -807.871520

description: Gaussian 16 (C01) calculation
DOI: 10.14469/hpc/11301
title: Catalyst regeneration step, addition of acid, TS4, Def2-SVPP, G = -788.512187

description: Gaussian 16 (C01) calculation
DOI: 10.14469/hpc/11303
title: TS3 for C-O break, rotamer, G = -807.871520, IRC

description: Gaussian 16 (C01) calculation
DOI: 10.14469/hpc/11306
title: Removal of H2O, catalyst regeneration step, Def2-SVPP, TS4, G = -788.512187, IRC

description: Gaussian 16 (C01) calculation
DOI: 10.14469/hpc/11352
title: Removal of OMe from B(OMe)3 by acetic acid, TS1, Def2-TZVPP, G = -828.779670

description: Gaussian 16 (C01) calculation
DOI: 10.14469/hpc/11308
title: Species 4, G = -807.919250

description: Gaussian 16 (C01) calculation
DOI: 10.14469/hpc/11367
title: Uses of B(OMe)3, G = -923.491815, IRC

description: Gaussian 16 (C01) calculation
DOI: 10.14469/hpc/11678
title: Removal of OMe from B(OMe)3 by acetic acid, TS1, G = -827.764488, IRC =&gt; Intermediate 2, G = -827.767926

description: Gaussian 16 (C01) calculation
DOI: 10.6084/m9.figshare.22241542
title: VCaP_ATAC_ENZ3w_100nM-Dex_rep1

description: VCaP_ATAC_ENZ3w_100nM-Dex_rep1
DOI: 10.6084/m9.figshare.22241542.v1
title: VCaP_ATAC_ENZ3w_100nM-Dex_rep1

description: VCaP_ATAC_ENZ3w_100nM-Dex_rep1
DOI: 10.6084/m9.figshare.22241551
title: VCaP_ATAC_ENZ3w_100nM-Dex_rep2

description: VCaP_ATAC_ENZ3w_100nM-Dex_rep2
DOI: 10.6084/m9.figshare.22241551.v1
title: VCaP_ATAC_ENZ3w_100nM-Dex_rep2

description: VCaP_ATAC_ENZ3w_100nM-Dex_rep2
DOI: 10.11588/data/lb6j0j/3mrhs1
title: 68-Schoenenberg-SI-Tab-3.csv

description: :unav
DOI: 10.11588/data/lb6j0j/xh9sy0
title: 68-Schoenenberg-SI-Tab-2.tab

description: :unav
DOI: 10.11588/data/lb6j0j/uxagi8
title: 68-Schoenenberg-SI-Tab-1.tab

description: :unav
DOI: 10.11588/data/lb6j0j/vtetbo
title: 68-Schoenenberg-SI-Tab-3.txt

description: :unav
DOI: 10.11588/data/lb6j0j
title: Ergänzungsmaterial zu: Diachronic Perspectives on Upper Palaeolithic Landscape Accessibility / Jungpaläolithische Landschafts-Akzessibilität im diachronen Vergleich

description: Hunter-gatherer communities are highly dependent on the accessibility of their surrounding landscapes. Relief, as well as the predominant vegetation strongly influence walking speed and thus the size of foraging ranges around camp sites: the catchments. Throughout the Upper Palaeolithic, landscapes are shaped by various climatic developments, requiring adaptations of subsistence strategies. A diachronic and supra-regional comparison of catchment sizes promises to shed light on such adaptive processes. This study seeks to model Upper Palaeolithic site catchments in consideration of different landcovers, depending on changing climatic conditions in Western and Central Europe. Such large-scale comparisons of catchment sizes have not yet been the topic of extensive research. As we are now able to show, changes in vegetation density led to a greater restriction of catchment sizes. This is partially compensated by the preferred settlement of level regions. The climatic shift between the Last Glacial Maximum and the Late Glacial is known to have various effects on demography, tool technology and the mobility patterns of hunter-gatherer societies. This picture can now be complemented by one additional aspect: the adaptation of mobility as a response to changing landscape accessibility and its impact on land-use.
DOI: 10.6084/m9.figshare.22241566
title: VCaP_ATAC_ENZ3w_naked-DNA_rep1

description: VCaP_ATAC_ENZ3w_naked-DNA_rep1
DOI: 10.6084/m9.figshare.22241566.v1
title: VCaP_ATAC_ENZ3w_naked-DNA_rep1

description: VCaP_ATAC_ENZ3w_naked-DNA_rep1
DOI: 10.5281/zenodo.5379544
title: Protein length distribution is remarkably consistent across Life

description: Supplementary Files. Supplementary Files 1 - LengthAnalysis_Data.tar.gz Archive containing the dataset used in this study as well as a curated and annotated Jupyter Notebook used for data analysis, along with temporary pickle files that can be used to skip expensive computation.[March 2023: Updated with additional analyses] Supplementary Files 2 - long_proteins.tar.gz Archive containing the dataset and Jupyter Notebook used for the Gene Ontology enrichment analysis of long proteins in genomes with atypical protein length distributions. Supplementary Files 3 - AllSpecies_Distributions_Figures.tar.gz Archive containing a graphical representation of protein length distribution for each individual proteome in the dataset, as png files.
DOI: 10.5281/zenodo.5379545
title: Protein length distribution is remarkably consistent across Life

description: Supplementary Files. Supplementary Files 1 - LengthAnalysis_Data.tar.gz Archive containing the dataset used in this study as well as a curated and annotated Jupyter Notebook used for data analysis, along with temporary pickle files that can be used to skip expensive computation. Supplementary Files 2 - long_proteins.tar.gz Archive containing the dataset and Jupyter Notebook used for the Gene Ontology enrichment analysis of long proteins in genomes with atypical protein length distributions. Supplementary Files 3 - AllSpecies_Distributions_Figures.tar.gz Archive containing a graphical representation of protein length distribution for each individual proteome in the dataset, as png files.
DOI: 10.5281/zenodo.7712057
title: Protein length distribution is remarkably consistent across Life

description: Supplementary Files. Supplementary Files 1 - LengthAnalysis_Data.tar.gz Archive containing the dataset used in this study as well as a curated and annotated Jupyter Notebook used for data analysis, along with temporary pickle files that can be used to skip expensive computation.[March 2023: Updated with additional analyses] Supplementary Files 2 - long_proteins.tar.gz Archive containing the dataset and Jupyter Notebook used for the Gene Ontology enrichment analysis of long proteins in genomes with atypical protein length distributions. Supplementary Files 3 - AllSpecies_Distributions_Figures.tar.gz Archive containing a graphical representation of protein length distribution for each individual proteome in the dataset, as png files.
DOI: 10.6084/m9.figshare.22241584
title: VCaP_ATAC_naked-DNA_rep1

description: VCaP_ATAC_naked-DNA_rep1
DOI: 10.6084/m9.figshare.22241584.v1
title: VCaP_ATAC_naked-DNA_rep1

description: VCaP_ATAC_naked-DNA_rep1
DOI: 10.5519/qd.x1leq4vn
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (0 records)