cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.4487289
title: Publications Dataset

description: Metadata for the complete set of all PubMed records through 2012 (with part of 2013 available as well), including title, authors, and year of publication. All data provided originates from NLM’s PubMed database (as downloaded April 24, 2013 from the NLM FTP site) and was retrieved via the Scholarly Database. Source: Scholarly Database. Date range: 1809 to 2013. File size: 21.5M publications and 10.8M authors; 3.1GB uncompressed Please cite: Robert P. Light, David E. Polley and Katy Börner. Open Data and Open Code for Big Science of Science Studies. In Proc. Intl. Society of Scientometrics and Informetrics Conf., pp 1342-1356, 2013. Gavin La Rowe, Sumeet Adinath Ambre, John W. Burgoon, Weimao Ke, and Katy Börner. The Scholarly Database and its Utility for Scientometrics Research. Scientometrics, 79.2 (2009): 219-234.
DOI: 10.6084/m9.figshare.13271713
title: Lineage through time analyses have their limitations: the case of the New Zealand flora

description: Lineage through time plots (LTTs) are often used to explore past patterns of lineage diversification and community assembly. However, as they are based solely on extant species their ability to accurately depict past events can be questioned. Here, simulation models based on neutral processes are used to explore immigration and extinction scenarios to assist with interpretation of LTT plots generated from molecular clock age estimates for a nearly complete set of extant New Zealand vascular plant genera. With significant genus turnover, model simulations yield smooth exponential and linear semi-log LTT plots. Abrupt changes in extinction and immigration rates imposed in the scenarios caused only slight alterations of the curves. The vast majority of New Zealand vascular plant genera derive from trans-oceanic dispersal, and LTT plots generated from divergence dates and fossil data indicate consistently high turnover. Even major geological and climatic events leave minor signatures on LTT plots. Most notably, the maximum Oligocene Marine Transgression (27–22 Ma), when at least 85% of the current landmass was inundated, isn’t clearly registered. By themselves, LTT plots shed little light on the biotic effects of climatic or geomorphic change in the remote past and need to be interpreted in the light of fossil and geological data.
DOI: 10.6084/m9.figshare.13271713.v1
title: Lineage through time analyses have their limitations: the case of the New Zealand flora

description: Lineage through time plots (LTTs) are often used to explore past patterns of lineage diversification and community assembly. However, as they are based solely on extant species their ability to accurately depict past events can be questioned. Here, simulation models based on neutral processes are used to explore immigration and extinction scenarios to assist with interpretation of LTT plots generated from molecular clock age estimates for a nearly complete set of extant New Zealand vascular plant genera. With significant genus turnover, model simulations yield smooth exponential and linear semi-log LTT plots. Abrupt changes in extinction and immigration rates imposed in the scenarios caused only slight alterations of the curves. The vast majority of New Zealand vascular plant genera derive from trans-oceanic dispersal, and LTT plots generated from divergence dates and fossil data indicate consistently high turnover. Even major geological and climatic events leave minor signatures on LTT plots. Most notably, the maximum Oligocene Marine Transgression (27–22 Ma), when at least 85% of the current landmass was inundated, isn’t clearly registered. By themselves, LTT plots shed little light on the biotic effects of climatic or geomorphic change in the remote past and need to be interpreted in the light of fossil and geological data.
DOI: 10.6084/m9.figshare.13553721.v1
title: Spore viability and germination of some ectomycorrhizal fungi from New Zealand and implications for forest restoration

description: Ectomycorrhizal fungi (EMF) are critical to the establishment of many plant species and an important consideration in ecological restoration of southern beech (Nothofagaceae) forest. However, information on spore viability and storage is lacking for EMF taxa associated with southern beech. This study tested the viability and germination of spores from fruiting bodies collected during autumn and spring from mountain beech forest, Otago, New Zealand. Nuclear ribosomal ITS sequences matched autumn collections to the EMF genera <i>Cortinarius, Inocybe</i> and <i>Russula,</i> but all spring collections were an undescribed hypogeous taxon resembling the native EMF genus <i>Hysterangium</i>, referred to here as Hysterangiaceae ‘Motatapu’. We investigated propidium iodide as a spore viability test, and compared spore germination in water vs glucose, in different temperature and light regimes, and between freshly collected spores and spores from fruiting bodies dried at 30°C or frozen at −20°C. Propidium iodide did not stain all devitalised spores, so may be unreliable for quantifying viability of fresh spores. Spore germination in water was &lt;6% for all genera and &lt;2% for most taxon × treatment combinations. Fresh spores of Hysterangiaceae ‘Motatapu’ suspended in 4°C water showed higher germination than at 20°C; excluding light had no significant effect. Spores of the same taxon suspended in 10% and 20% glucose showed lower germination in comparison to water and showed deformations. Germination percentages of all taxa decreased with storage, but spores of some taxa retained viability for 120 days in 4°C water suspensions. Spores of Hysterangiaceae ‘Motatapu’ showed the least loss of viability with storage of all taxa investigated. For the purposes of storing EMF material for use as inoculum, we recommend drying fruiting bodies at 30°C for storage, then preparing fresh spore suspensions in water when inoculum is required.
DOI: 10.6084/m9.figshare.13553721
title: Spore viability and germination of some ectomycorrhizal fungi from New Zealand and implications for forest restoration

description: Ectomycorrhizal fungi (EMF) are critical to the establishment of many plant species and an important consideration in ecological restoration of southern beech (Nothofagaceae) forest. However, information on spore viability and storage is lacking for EMF taxa associated with southern beech. This study tested the viability and germination of spores from fruiting bodies collected during autumn and spring from mountain beech forest, Otago, New Zealand. Nuclear ribosomal ITS sequences matched autumn collections to the EMF genera <i>Cortinarius, Inocybe</i> and <i>Russula,</i> but all spring collections were an undescribed hypogeous taxon resembling the native EMF genus <i>Hysterangium</i>, referred to here as Hysterangiaceae ‘Motatapu’. We investigated propidium iodide as a spore viability test, and compared spore germination in water vs glucose, in different temperature and light regimes, and between freshly collected spores and spores from fruiting bodies dried at 30°C or frozen at −20°C. Propidium iodide did not stain all devitalised spores, so may be unreliable for quantifying viability of fresh spores. Spore germination in water was &lt;6% for all genera and &lt;2% for most taxon × treatment combinations. Fresh spores of Hysterangiaceae ‘Motatapu’ suspended in 4°C water showed higher germination than at 20°C; excluding light had no significant effect. Spores of the same taxon suspended in 10% and 20% glucose showed lower germination in comparison to water and showed deformations. Germination percentages of all taxa decreased with storage, but spores of some taxa retained viability for 120 days in 4°C water suspensions. Spores of Hysterangiaceae ‘Motatapu’ showed the least loss of viability with storage of all taxa investigated. For the purposes of storing EMF material for use as inoculum, we recommend drying fruiting bodies at 30°C for storage, then preparing fresh spore suspensions in water when inoculum is required.
DOI: 10.5281/zenodo.4050559
title: CESM1 2015 Cold Blob Sensitivity Experiments

description: CESM1-DPLE Hindcast Sensitivity Experiments from Maroon et al. (2021) The files in this repository include CESM sensitivity experiment output shown in Maroon et al. (2021). Descriptions of the protocols for each of the experiments can be found in the paper. Each individual compressed file here corresponds to one of the sensitivity experiments. Individual netcdf files are in standard CESM1 time series format using CESM1 naming convention. Each included variable has its own folder and inside there is one netcdf file for each ensemble member. Please contact the authors if you have any difficulty opening the files or figuring out which files go with which sensitivity experiments (emaroon@wisc.edu). Maroon, E. A., Yeager, S. G., Danabasoglu, G., & Rosenbloom, N. (2021). Was the 2015 North Atlantic subpolar cold anomaly predictable?, Journal of Climate, https://doi.org/10.1175/JCLI-D-20-0750.1
description: {"references": ["https://doi.org/10.1175/JCLI-D-20-0750.1"]}
DOI: 10.5281/zenodo.4050558
title: CESM1 2015 Cold Blob Sensitivity Experiments

description: CESM1-DPLE Hindcast Sensitivity Experiments from Maroon et al. (2021) The files in this repository include CESM sensitivity experiment output shown in Maroon et al. (2021). Descriptions of the protocols for each of the experiments can be found in the paper. Each individual compressed file here corresponds to one of the sensitivity experiments. Individual netcdf files are in standard CESM1 time series format using CESM1 naming convention. Each included variable has its own folder and inside there is one netcdf file for each ensemble member. Please contact the authors if you have any difficulty opening the files or figuring out which files go with which sensitivity experiments (emaroon@wisc.edu). Maroon, E. A., Yeager, S. G., Danabasoglu, G., & Rosenbloom, N. (2021). Was the 2015 North Atlantic subpolar cold anomaly predictable?, Journal of Climate, https://doi.org/10.1175/JCLI-D-20-0750.1
description: {"references": ["https://doi.org/10.1175/JCLI-D-20-0750.1"]}
DOI: 10.5281/zenodo.4747734
title: anonymous

description: anonymous
DOI: 10.5281/zenodo.4747733
title: anonymous

description: anonymous
DOI: 10.5281/zenodo.4747795
title: LCTSC DICOM & NIFTI Test Data

description: This data is a portion of the LCTSC dataset provided by The Cancer Imaging Archive (TCIA) and is<br> released under the Creative Commons Attribution 3.0 Unported License. Citations & Data Usage Policy <br> Users of this data must abide by the TCIA Data Usage Policy and the Creative Commons Attribution <br> 3.0 Unported License under which it has been published. Attribution should include references to <br> the following citations: Dataset Citation<br> Yang, Jinzhong; Sharp, Greg; Veeraraghavan, Harini ; van Elmpt, Wouter ; Dekker, Andre; Lustberg, Tim; Gooding, Mark. (2017). Data from Lung CT Segmentation Challenge. The Cancer Imaging Archive. http://doi.org/10.7937/K9/TCIA.2017.3r3fvz08 Publication Citation<br> Yang, J. , Veeraraghavan, H. , Armato, S. G., Farahani, K. , Kirby, J. S., Kalpathy‐Kramer, J. , van Elmpt, W. , Dekker, A. , Han, X. , Feng, X. , Aljabar, P. , Oliveira, B. , van der Heyden, B. , Zamdborg, L. , Lam, D. , Gooding, M. and Sharp, G. C. (2018), Autosegmentation for thoracic radiation treatment planning: A grand challenge at AAPM 2017. Med. Phys.. . doi: 10.1002/mp.13141 TCIA Citation<br> Clark K, Vendt B, Smith K, Freymann J, Kirby J, Koppel P, Moore S, Phillips S, Maffitt D, Pringle M, Tarbox L, Prior F. The Cancer Imaging Archive (TCIA): Maintaining and Operating a Public Information Repository, Journal of Digital Imaging, Volume 26, Number 6, December, 2013, pp 1045-1057. (paper)
DOI: 10.5281/zenodo.4747794
title: LCTSC DICOM & NIFTI Test Data

description: This data is a portion of the LCTSC dataset provided by The Cancer Imaging Archive (TCIA) and is<br> released under the Creative Commons Attribution 3.0 Unported License. Citations & Data Usage Policy <br> Users of this data must abide by the TCIA Data Usage Policy and the Creative Commons Attribution <br> 3.0 Unported License under which it has been published. Attribution should include references to <br> the following citations: Dataset Citation<br> Yang, Jinzhong; Sharp, Greg; Veeraraghavan, Harini ; van Elmpt, Wouter ; Dekker, Andre; Lustberg, Tim; Gooding, Mark. (2017). Data from Lung CT Segmentation Challenge. The Cancer Imaging Archive. http://doi.org/10.7937/K9/TCIA.2017.3r3fvz08 Publication Citation<br> Yang, J. , Veeraraghavan, H. , Armato, S. G., Farahani, K. , Kirby, J. S., Kalpathy‐Kramer, J. , van Elmpt, W. , Dekker, A. , Han, X. , Feng, X. , Aljabar, P. , Oliveira, B. , van der Heyden, B. , Zamdborg, L. , Lam, D. , Gooding, M. and Sharp, G. C. (2018), Autosegmentation for thoracic radiation treatment planning: A grand challenge at AAPM 2017. Med. Phys.. . doi: 10.1002/mp.13141 TCIA Citation<br> Clark K, Vendt B, Smith K, Freymann J, Kirby J, Koppel P, Moore S, Phillips S, Maffitt D, Pringle M, Tarbox L, Prior F. The Cancer Imaging Archive (TCIA): Maintaining and Operating a Public Information Repository, Journal of Digital Imaging, Volume 26, Number 6, December, 2013, pp 1045-1057. (paper)
DOI: 10.6084/m9.figshare.14569476
title: DNA_and_RT_viruses.fasta

description: Discovery and characterization of actively replicating DNA and retro-transcribing viruses in lower vertebrate hosts based on RNA sequencing
DOI: 10.6084/m9.figshare.14569476.v1
title: DNA_and_RT_viruses.fasta

description: Discovery and characterization of actively replicating DNA and retro-transcribing viruses in lower vertebrate hosts based on RNA sequencing
DOI: 10.6084/m9.figshare.14374496
title: Complete mitochondrial genome and phylogenetic analysis of the copper shark Carcharhinus brachyurus (Guenther, 1870)

description: <b>Supplementary Table 1:</b> PCR primers used for amplification of the copper shark (<i>Carcharhinus brachyurus</i>) mitogenome.<br><b>Supplementary Table 2:</b> Mitochondrial genome characteristics of copper shark (<i>Carcharhinus brachyurus</i>).<br><b>Supplementary Table 3:</b> The complete mitogenomes of Carcharhinidae used for orthologous average nucleotide identity (OrthoANI) and phylogenetic analysis conducted in this study.<br>
DOI: 10.6084/m9.figshare.14374496.v1
title: Complete mitochondrial genome and phylogenetic analysis of the copper shark Carcharhinus brachyurus (Guenther, 1870)

description: <b>Supplementary Table 1:</b> PCR primers used for amplification of the copper shark (<i>Carcharhinus brachyurus</i>) mitogenome.<br><b>Supplementary Table 2:</b> Mitochondrial genome characteristics of copper shark (<i>Carcharhinus brachyurus</i>).<br><b>Supplementary Table 3:</b> The complete mitogenomes of Carcharhinidae used for orthologous average nucleotide identity (OrthoANI) and phylogenetic analysis conducted in this study.<br>
DOI: 10.6084/m9.figshare.14569473
title: Project_TENM4

description: In this study, all individuals with SCZ were interviewed by at least two independent psychiatrists. Diagnoses were made strictly according to Diagnostic and Statistical Manual of Mental Disorders (DSM)-IV criteria, and patients with other neurological, mental or psychiatric disorders, or with history of drug use were excluded. All participants provided written informed consent. Approval was received for our study from the Ethics Committee of Human Genetic Resources of Shanghai Jiao Tong University and local hospitals. For the family-based sequencing study, a total 68 SCZ families with no less than 3 patients were selected, and a total 351 samples were collected for targeted sequencing.
DOI: 10.6084/m9.figshare.14569473.v1
title: Project_TENM4

description: In this study, all individuals with SCZ were interviewed by at least two independent psychiatrists. Diagnoses were made strictly according to Diagnostic and Statistical Manual of Mental Disorders (DSM)-IV criteria, and patients with other neurological, mental or psychiatric disorders, or with history of drug use were excluded. All participants provided written informed consent. Approval was received for our study from the Ethics Committee of Human Genetic Resources of Shanghai Jiao Tong University and local hospitals. For the family-based sequencing study, a total 68 SCZ families with no less than 3 patients were selected, and a total 351 samples were collected for targeted sequencing.
DOI: 10.6084/m9.figshare.14565018
title: Standardized Quantitative Results of Serum Metabolites

description: Standardized Quantitative Results of Serum Metabolites
DOI: 10.6084/m9.figshare.14565018.v1
title: Standardized Quantitative Results of Serum Metabolites

description: Standardized Quantitative Results of Serum Metabolites
DOI: 10.6084/m9.figshare.14564874
title: Standardized Quantitative Results of Feces metabolites

description: Standardized Quantitative Results of Feces metabolites<br>
DOI: 10.6084/m9.figshare.14564874.v1
title: Standardized Quantitative Results of Feces metabolites

description: Standardized Quantitative Results of Feces metabolites<br>
DOI: 10.25919/dc4m-z265
title: Environment-Production tradeoffs in subtropical crop rotations

description: This collection contains supporting information for the article "Design of sustainable dryland crop rotations require value judgements and efficient trade-offs" by Hochman et al. (2021)
DOI: 10.6084/m9.figshare.14564133
title: OTUs and microbial diversity analysis

description: Fecal contents collected were processed for 16S rRNA metagenomic analysis, and OTUs
DOI: 10.6084/m9.figshare.14569503.v1
title: Raw data for peat DOM

description: This is the raw data used for creating figures in the manuscript.
DOI: 10.6084/m9.figshare.14569425
title: Rojahn et al ( 2021) - Freshwater Biology Data.xlsx

description: Supplementary material: The value of quantitative environmental DNA analyses for the management of invasive and endangered fish. <br>Datasheets contain site sample information, conventional monitoring data (catch and electrofishing data) and raw quantitative PCR data used in analyses.
DOI: 10.6084/m9.figshare.13502306.v1
title: Examination of the usability of leaf chlorophyll content and gene expression analyses as nitrogen status biomarkers in <i>Sorghum bicolor</i>

description: Sorghum [<i>Sorghum bicolor</i> (L.) Moench] has been receiving attention as a feedstock for biomass energy. Since nitrogen (N) significantly affects the plant biomass production, diagnosing the N status of sorghum during its growth would be significant. Therefore, in this study, we analyzed the changes in several physiological parameters of sorghum in response to N limitation, with the aim of identifying candidates of N status biomarkers in this species. Parameters responding early and sensitively to N deficiency were searched in hydroponically cultured seedlings, and their applicability to field conditions was examined. We found that the leaf chlorophyll content measured as a soil-plant analysis development (SPAD) value was promising as a candidate N status biomarker, as it showed responses consistent with N regimes in field conditions in multiple genotypes. A gene expression analysis was capable of detecting N deficiency sensitively at an early stage, although its application to practical situations requires further investigation to identify a suitable sets of marker genes.
DOI: 10.6084/m9.figshare.13502306
title: Examination of the usability of leaf chlorophyll content and gene expression analyses as nitrogen status biomarkers in <i>Sorghum bicolor</i>

description: Sorghum [<i>Sorghum bicolor</i> (L.) Moench] has been receiving attention as a feedstock for biomass energy. Since nitrogen (N) significantly affects the plant biomass production, diagnosing the N status of sorghum during its growth would be significant. Therefore, in this study, we analyzed the changes in several physiological parameters of sorghum in response to N limitation, with the aim of identifying candidates of N status biomarkers in this species. Parameters responding early and sensitively to N deficiency were searched in hydroponically cultured seedlings, and their applicability to field conditions was examined. We found that the leaf chlorophyll content measured as a soil-plant analysis development (SPAD) value was promising as a candidate N status biomarker, as it showed responses consistent with N regimes in field conditions in multiple genotypes. A gene expression analysis was capable of detecting N deficiency sensitively at an early stage, although its application to practical situations requires further investigation to identify a suitable sets of marker genes.
DOI: 10.6084/m9.figshare.13278023
title: Silicon modulates expression of pathogen defense-related genes during alleviation of copper toxicity in <i>Nicotiana tabacum</i>

description: Plants treated with metals better fend off infection by pathogens. This activity is mediated, at least in part, by the activation of the salicylic acid (SA) signaling pathway. Previous work in our laboratory demonstrated that silicon (Si) could alleviate copper (Cu) toxicity stress in <i>Nicotiana tabacum</i>. However, how Si affected expression of genes involved in SA biosynthesis and signaling in <i>N. tabacum</i> under Cu stress was unclear. Therefore, we investigated this at two time points. Roots of plants treated with Cu toxicity for one week exhibited increased transcript levels for <i>Isochorismate Synthase1</i>, a gene encoding a key enzyme involved in SA biosynthesis and the addition of Si further enhanced expression. Microarray analysis identified a number of disease defense-associated genes up-regulated in <i>N. tabacum</i> roots after one week of Cu toxicity treatment and further increased when plants were also supplemented with Si. However, the effect of Si on expression of these genes was lost after three weeks of treatment, indicating these effects are dynamic.
DOI: 10.6084/m9.figshare.13278023.v1
title: Silicon modulates expression of pathogen defense-related genes during alleviation of copper toxicity in <i>Nicotiana tabacum</i>

description: Plants treated with metals better fend off infection by pathogens. This activity is mediated, at least in part, by the activation of the salicylic acid (SA) signaling pathway. Previous work in our laboratory demonstrated that silicon (Si) could alleviate copper (Cu) toxicity stress in <i>Nicotiana tabacum</i>. However, how Si affected expression of genes involved in SA biosynthesis and signaling in <i>N. tabacum</i> under Cu stress was unclear. Therefore, we investigated this at two time points. Roots of plants treated with Cu toxicity for one week exhibited increased transcript levels for <i>Isochorismate Synthase1</i>, a gene encoding a key enzyme involved in SA biosynthesis and the addition of Si further enhanced expression. Microarray analysis identified a number of disease defense-associated genes up-regulated in <i>N. tabacum</i> roots after one week of Cu toxicity treatment and further increased when plants were also supplemented with Si. However, the effect of Si on expression of these genes was lost after three weeks of treatment, indicating these effects are dynamic.