cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.4121/6affb4a6-2893-41e8-bdf8-d276247d7d19
title: Oxford Nanopore long-read genome sequencing of mutants in Streptococcus suis strain P1/7 constructed using pSStarget, a novel plasmid-based CRISPR/Cas9 genome editing system

description: <strong>Description:</strong>This dataset contains ONT sequencing reads of the wild type strain <em>S. suis</em> P1/7 and four derived mutant strains constructed using a novel CRISPR-Cas9 genome editing system for S. suis. Our data shows that our laboratory stock of strain P1/7 has 2 SNPs and a 5 bp deletion relative to the reference sequence (AM946016.1) published in GenBank. We confirm that the precise deletion of the <em>cpsEF </em>and s<em>ly</em> genes in the respective mutants as well as in the double knockout mutant. Moreover, we confirm the precise introduction of targeted mutations resulting in a single amino acid change in the Enolase gene product. No other mutations or structural variations have been detected. <strong>This dataset contains the following 5 files:</strong>WT_raw_reads.fastq.gz dCps_raw_reads.fastq.gz dSly_raw_reads.fastq.gz dCps_dSly_raw_reads.fastq.gz enoK261A_raw_reads.fastq.gz <strong>Explanation of variables:</strong>All files contain raw ONT reads in the FASTQ (.fq) format in zipped (.gz) format.WT refers to the wild type strain Streptococcus suis P1/7. The prefix dCps and dSly refers to a knockout strain with the <em>cpsE/cpsF</em> and <em>sly</em> genes deleted, respectively. The double knockout mutant, in which both loci were deleted, is denoted with the prefix dCps_dSly. Finally, prefix enoK261A denotes the strain with a single amino acid mutation in the essential <em>eno</em> gene.<br><strong>Materials and methods:</strong>All strains were grown in Todd-Hewitt broth (Oxoid) supplemented with 0.2% Bacto™ yeast extract (BD Biosciences) (THY) without agitation. Overnight cultures (10ml) were harvested by centrifugation at 4500x for 10min and the pellets were transferred to bead beating tubes tube containing 0.1mm silica beads (Lysing matrix B, MP Biomedicals) and lysed by bead beating for 40 seconds at 4.0 m/s using a FastPrep-24 5G (MP Biomedicals). The lysates were cleared by centrifugation at 16.000x for 10 minutes and the genomic DNA (gDNA) has been isolated using the PowerSoil DNA Isolation Kit (Qiagen) according to manufacturer’s instructions. The concentration, purity and integrity of the extracted gDNA were determined using the Qubit BR DNA assay, DeNovix spectrophotometer and gel electrophoresis, respectively. The concentrations were normalized to 50ng/μl and sent to Plasmidsaurus (https://www.plasmidsaurus.com/) for further processing. Briefly, genomic DNA was minimally fragmented, amplification-free libraries were constructed from the fragmented DNA using the v14 library prep chemistry and the libraries were sequenced using R10.4.1 flow cells. The raw reads have been delivered in FASTQ format.<br><strong>License</strong>This dataset is published under the CC BY-SA (Attribution ShareAlike) license.<br>
DOI: 10.4121/6affb4a6-2893-41e8-bdf8-d276247d7d19.v2
title: Oxford Nanopore long-read genome sequencing of mutants in Streptococcus suis strain P1/7 constructed using pSStarget, a novel plasmid-based CRISPR/Cas9 genome editing system

description: <strong>Description:</strong>This dataset contains ONT sequencing reads of the wild type strain <em>S. suis</em> P1/7 and four derived mutant strains constructed using a novel CRISPR-Cas9 genome editing system for S. suis. Our data shows that our laboratory stock of strain P1/7 has 2 SNPs and a 5 bp deletion relative to the reference sequence (AM946016.1) published in GenBank. We confirm that the precise deletion of the <em>cpsEF </em>and s<em>ly</em> genes in the respective mutants as well as in the double knockout mutant. Moreover, we confirm the precise introduction of targeted mutations resulting in a single amino acid change in the Enolase gene product. No other mutations or structural variations have been detected. <strong>This dataset contains the following 5 files:</strong>WT_raw_reads.fastq.gz dCps_raw_reads.fastq.gz dSly_raw_reads.fastq.gz dCps_dSly_raw_reads.fastq.gz enoK261A_raw_reads.fastq.gz <strong>Explanation of variables:</strong>All files contain raw ONT reads in the FASTQ (.fq) format in zipped (.gz) format.WT refers to the wild type strain Streptococcus suis P1/7. The prefix dCps and dSly refers to a knockout strain with the <em>cpsE/cpsF</em> and <em>sly</em> genes deleted, respectively. The double knockout mutant, in which both loci were deleted, is denoted with the prefix dCps_dSly. Finally, prefix enoK261A denotes the strain with a single amino acid mutation in the essential <em>eno</em> gene.<br><strong>Materials and methods:</strong>All strains were grown in Todd-Hewitt broth (Oxoid) supplemented with 0.2% Bacto™ yeast extract (BD Biosciences) (THY) without agitation. Overnight cultures (10ml) were harvested by centrifugation at 4500x for 10min and the pellets were transferred to bead beating tubes tube containing 0.1mm silica beads (Lysing matrix B, MP Biomedicals) and lysed by bead beating for 40 seconds at 4.0 m/s using a FastPrep-24 5G (MP Biomedicals). The lysates were cleared by centrifugation at 16.000x for 10 minutes and the genomic DNA (gDNA) has been isolated using the PowerSoil DNA Isolation Kit (Qiagen) according to manufacturer’s instructions. The concentration, purity and integrity of the extracted gDNA were determined using the Qubit BR DNA assay, DeNovix spectrophotometer and gel electrophoresis, respectively. The concentrations were normalized to 50ng/μl and sent to Plasmidsaurus (https://www.plasmidsaurus.com/) for further processing. Briefly, genomic DNA was minimally fragmented, amplification-free libraries were constructed from the fragmented DNA using the v14 library prep chemistry and the libraries were sequenced using R10.4.1 flow cells. The raw reads have been delivered in FASTQ format.<br><strong>License</strong>This dataset is published under the CC BY-SA (Attribution ShareAlike) license.<br>
DOI: 10.20372/eiar-rdm/9yaiis
title: GIZ_ Integrated Soil Fertility Management (ISFM)_crop response dataset

description: Although soil and agronomy data collection in Ethiopia has begun over 60 years ago, the data are hardly accessible as they are scattered across different organizations, mostly held in the hands of individuals (Ashenafi et al.,2020; Tamene et al.,2022), which makes them vulnerable to permanent loss. Cognizant of the problem, the Coalition of the Willing (CoW) for data sharing and access was created in 2018 with joint support and coordination of the Alliance Bioversity-CIAT and GIZ (https://www.ethioagridata.com/index.html). Mobilizing its members, the CoW has embarked on data rescue operations including data ecosystem mapping, collation, and curation of the legacy data, which was put into the central data repository for its members and the wider data user’s community according to the guideline developed based on the FAIR data principles and approved by the CoW. So far, CoW managed to collate and rescue about 20,000 legacy soil profile data and over 38,000 crop responses to fertilizer data (Tamene et al.,2022). The crop response dataset (N=436 observations) is extracted, transformed, and uploaded into a harmonized template, consisting of 76 variables. GIZ_ Integrated Soil Fertility Management (ISFM)_crop response data. Reference: Ashenafi, A., Tamene, L., and Erkossa, T. 2020. Identifying, Cataloguing, and Mapping Soil and Agronomic Data in Ethiopia. CIAT Publication No. 506. International Center for Tropical Agriculture (CIAT). Addis Ababa, Ethiopia. 42 p. 10.13140/RG.2.2.31759.41123. Tamene L; Erkossa T; Tafesse T; Abera W; Schultz S. 2021. A coalition of the Willing - Powering data-driven solutions for Ethiopian Agriculture. CIAT Publication No. 518. International Center for Tropical Agriculture (CIAT). Addis Ababa, Ethiopia. 34 p. https://www.ethioagridata.com/Resources/Powering%20Data-Driven%20Solutions%20for%20Ethiopian%20Agriculture.pdf. The Coalition of the Willing (CoW) website: https://www.ethioagridata.com/index.html. TERMS: Access to the data is limited to the CoW members until the national soil and agronomy data-sharing directive of MoA is registered by the Ministry of Justice and released for implementation. DISCLAIMER: The dataset populated in the harmonized template consisting of 76 variables is extracted, transformed, and uploaded from the source document by the CoW. Hence, if any irregularities are observed, the data users have referred to the source document uploaded along with the dataset. Use of the dataset and any consequences arising from using it is the user’s sole responsibility.
DOI: 10.6084/m9.figshare.21982508.v1
title: Supplementary Materials for "Incomplete-lineage sorting explains the low performance of DNA barcoding in a radiation of four species of Western European grasshoppers (Orthoptera: Acrididae : <em>Chorthippus</em>)"

description: This is the supplementary material of Nabholz : "Incomplete-lineage sorting explains the low performance of DNA barcoding in a radiation of four species of Western European grasshoppers (Orthoptera: Acrididae : <em>Chorthippus</em>)". This includes : 1. Supplementary figure S1 to S7 2. Supplementary Table S1 & S2 3. Caelifera.TimeTree.tree : Caelifera time tree with branch length in 10 Myr units and 95% credibility confidence intervals obtained by MCMCTREE analysis. 4. Folder seq_data contains : Phylogeny folder : Alignments used for phylogenetic reconstruction and mutation rate estimation. Pop_gen folder : Alignments used for population genetic analyses.
DOI: 10.6084/m9.figshare.21982508
title: Supplementary Materials for "Incomplete-lineage sorting explains the low performance of DNA barcoding in a radiation of four species of Western European grasshoppers (Orthoptera: Acrididae : <em>Chorthippus</em>)"

description: This is the supplementary material of Nabholz : "Incomplete-lineage sorting explains the low performance of DNA barcoding in a radiation of four species of Western European grasshoppers (Orthoptera: Acrididae : <em>Chorthippus</em>)". This includes : 1. Supplementary figure S1 to S7 2. Supplementary Table S1 & S2 3. Caelifera.TimeTree.tree : Caelifera time tree with branch length in 10 Myr units and 95% credibility confidence intervals obtained by MCMCTREE analysis. 4. Folder seq_data contains : Phylogeny folder : Alignments used for phylogenetic reconstruction and mutation rate estimation. Pop_gen folder : Alignments used for population genetic analyses.
DOI: 10.6084/m9.figshare.24031989.v1
title: Rawdata.csv

description: Data for manuscript 'Nitrogen-induced acidification modulates soil biodiversity-function relationships'.
DOI: 10.57841/casdc.0001965
title: 圆锥滚子轴承润滑与动力学耦合研究
DOI: 10.6084/m9.figshare.21859809
title: Supplementary material from "Changes in pattern of plant-insect interactions on the Persian ironwood (Parrotia persica, Hamamelidaceae) over the last 3 million years"

description: The Hyrcanian forest is composed of many Arcto-Tertiary plant species that since the beginning of the Quaternary glaciations have decreased their distribution until they became endemic to the coasts of the Caspian Sea in the northern part of Iran. Today, the Hyrcanian forest is considered as the closest similar remnant of the Plio-Pleisto- cene European paleoforests. One of the most emblematic plant species is the Persian Ironwood (Parrotia persica C. A. Mey). This study presents the first comparison of plant-insect interaction patterns between modern samples from the current Persian Ironwood populations of the endemic species to the Hyrcanian forest and the fossil counterpart from Willershausen (Germany) and Bernasso (France). We wanted to know if the ecological rela- tionships of P. persica with its environment were similar or changed during the last few millions of years, through the analysis of their plant-insect interaction. Fifteen sites were selected in the Hyrcanian forest along temperature and precipitation gradients. A total of 2160 leaves were collected, measured, and examined through some leaf characteristics and their plant-insect interactions. 84% of the leaves were damaged and a total of 3507 damage occurrences were found. A significant lower proportion of specialized damages were found on the leaves from P. persica in the Hyrcanian forest compared to what we observed among the samples from the two fossil outcrops, which could suggest a “non-optimal” environment for P. persica today in its current endemic distribution.
DOI: 10.6084/m9.figshare.21859809.v1
title: Supplementary material from "Changes in pattern of plant-insect interactions on the Persian ironwood (Parrotia persica, Hamamelidaceae) over the last 3 million years"

description: The Hyrcanian forest is composed of many Arcto-Tertiary plant species that since the beginning of the Quaternary glaciations have decreased their distribution until they became endemic to the coasts of the Caspian Sea in the northern part of Iran. Today, the Hyrcanian forest is considered as the closest similar remnant of the Plio-Pleisto- cene European paleoforests. One of the most emblematic plant species is the Persian Ironwood (Parrotia persica C. A. Mey). This study presents the first comparison of plant-insect interaction patterns between modern samples from the current Persian Ironwood populations of the endemic species to the Hyrcanian forest and the fossil counterpart from Willershausen (Germany) and Bernasso (France). We wanted to know if the ecological rela- tionships of P. persica with its environment were similar or changed during the last few millions of years, through the analysis of their plant-insect interaction. Fifteen sites were selected in the Hyrcanian forest along temperature and precipitation gradients. A total of 2160 leaves were collected, measured, and examined through some leaf characteristics and their plant-insect interactions. 84% of the leaves were damaged and a total of 3507 damage occurrences were found. A significant lower proportion of specialized damages were found on the leaves from P. persica in the Hyrcanian forest compared to what we observed among the samples from the two fossil outcrops, which could suggest a “non-optimal” environment for P. persica today in its current endemic distribution.
DOI: 10.5281/zenodo.8242506
title: Unveiling Transformation: Glacier Area Changes in Changra-Bhaga and Suru-Zanskar Basins (2000-2022), Western Himalaya

description: The dataset encompasses the temporal variations in glacier extents within the Suru-Zanskar Basin and the Chandra-Bhaga Basin, both integral parts of the Western Himalayan region. Within this dataset, a total of 45 representative glaciers were manually digitized for the years 2000, 2007, 2016, and 2022, using satellite imagery for the Suru-Zanskar Basin. Similarly, temporal glacier areas were calculated for 51 selected glaciers spanning the years 2000, 2009, 2016, and 2022 within the Chandra-Bhaga Basin. For the year 2000, the dataset comprises a recorded area of 913.77 km² for the Suru-Zanskar Basin and 608.95 km² for the Chandra-Bhaga Basin, respectively. This dataset forms an integral component of the manuscript titled "Divergent Temporal Glacier Responses in the Chandra-Bhaga and Suru-Zanskar Basins of the Indian Western Himalaya."
DOI: 10.5281/zenodo.8242507
title: Unveiling Transformation: Glacier Area Changes in Changra-Bhaga and Suru-Zanskar Basins (2000-2022), Western Himalaya

description: The dataset encompasses the temporal variations in glacier extents within the Suru-Zanskar Basin and the Chandra-Bhaga Basin, both integral parts of the Western Himalayan region. Within this dataset, a total of 45 representative glaciers were manually digitized for the years 2000, 2007, 2016, and 2022, using satellite imagery for the Suru-Zanskar Basin. Similarly, temporal glacier areas were calculated for 51 selected glaciers spanning the years 2000, 2009, 2016, and 2022 within the Chandra-Bhaga Basin. For the year 2000, the dataset comprises a recorded area of 913.77 km² for the Suru-Zanskar Basin and 608.95 km² for the Chandra-Bhaga Basin, respectively. This dataset forms an integral component of the manuscript titled "Divergent Temporal Glacier Responses in the Chandra-Bhaga and Suru-Zanskar Basins of the Indian Western Himalaya."
DOI: 10.5526/erdr-00000186
title: Fish exclusion experiment from Hengill, Iceland
DOI: 10.6084/m9.figshare.24032340
title: Data and R code for Nutrient-BEF study

description: Data and R code for manuscript 'Nitrogen-induced acidification modulates soil biodiversity-function relationships'.
DOI: 10.6084/m9.figshare.24032340.v1
title: Data and R code for Nutrient-BEF study

description: Data and R code for manuscript 'Nitrogen-induced acidification modulates soil biodiversity-function relationships'.
DOI: 10.57841/casdc.0001966
title: 宽温域环境中聚四氟乙烯及其复合材料摩擦学性能研究
DOI: 10.5517/cc118njh
title: CCDC 961636: Experimental Crystal Structure Determination

description: Related Article: Jin-Qi Ren, Qing-Zhu Jiao, Yi-Nuo Wang,Fang-Yuan Xu, Xiao-Shao Cheng, Zhong-Lu You|2014|Wuji Huaxue Xuebao|30|640|
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc12q2ql
title: CCDC 1004329: Experimental Crystal Structure Determination

description: Related Article: Krzysztof Brzezinski|2021|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc12q2rm
title: CCDC 1004330: Experimental Crystal Structure Determination

description: Related Article: Krzysztof Brzezinski|2021|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc12q2sn
title: CCDC 1004331: Experimental Crystal Structure Determination

description: Related Article: Krzysztof Brzezinski|2021|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc1q3x5x
title: CCDC 1582679: Experimental Crystal Structure Determination

description: Related Article: Timothy G. Carroll, Rachel Garwick, Joshua Telser, Guang Wu, Gabriel Ménard|2018|Organometallics|37|848|doi:10.1021/acs.organomet.7b00797
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc29kbdm
title: CCDC 2131820: Experimental Crystal Structure Determination

description: Related Article: Neha Kesharwani, Chanchal Haldar|2022|Polyhedron|219|115787|doi:10.1016/j.poly.2022.115787
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2825cx
title: CCDC 2087458: Experimental Crystal Structure Determination

description: Related Article: Chien-Tien Chen, Jih-Sen Ho, Shu-Chih Weng|2022|Inorg.Chem.|61|5595|doi:10.1021/acs.inorgchem.2c00231
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2brxwx
title: CCDC 2167950: Experimental Crystal Structure Determination

description: Related Article: Günther Horrer, Ivo Krummenacher, Sophie Mann, Holger Braunschweig, Udo Radius|2022|Dalton Trans.|51|11054|doi:10.1039/D2DT01250B
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2f42th
title: CCDC 2238256: Experimental Crystal Structure Determination

description: Related Article: Sukanya Bagchi, Sujit Kamilya, Sakshi Mehta, Subhankar Mandal, Arka Bandyopadhyay, Awadhesh Narayan, Subrata Ghosh, Abhishake Mondal|2023|Dalton Trans.|52|11335|doi:10.1039/D3DT01707A
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2f42vj
title: CCDC 2238257: Experimental Crystal Structure Determination

description: Related Article: Sukanya Bagchi, Sujit Kamilya, Sakshi Mehta, Subhankar Mandal, Arka Bandyopadhyay, Awadhesh Narayan, Subrata Ghosh, Abhishake Mondal|2023|Dalton Trans.|52|11335|doi:10.1039/D3DT01707A
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2f42ym
title: CCDC 2238260: Experimental Crystal Structure Determination

description: Related Article: Sukanya Bagchi, Sujit Kamilya, Sakshi Mehta, Subhankar Mandal, Arka Bandyopadhyay, Awadhesh Narayan, Subrata Ghosh, Abhishake Mondal|2023|Dalton Trans.|52|11335|doi:10.1039/D3DT01707A
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.