cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21357439
title: Effect of mustard cover crops on corn growth, yield and soil water storage in southwest Texas

description: Mustard cover crops can provide multiple soil health benefits but may adversely affect cash crops by depleting soil water. This was tested in a center-pivot irrigated corn cropping system in southwest Texas from 2018 to 2020. Changes in biomass growth of both the cover crops and corn, and soil water content in the root zone were monitored multiple times during the main growth periods of the crops. Upon termination, biomass production of cover crops averaged 4271 kg/ha, with equivalent nitrogen and phosphorus inputs to the soil of 92 kg/ha and 12 kg/ha, respectively. Over 2 years, water use during the main growth period of the mustard cover crops and the fallow area averaged at 1.4 mm/day and 1.1 mm/day, respectively, and water use of corn following the mustard and fallow averaged at 4.0 mm/day and 3.7 mm/day, respectively, although the differences were only marginally significant. Our data suggest that water use of cover crops was affected by their growth patterns. The mustard cover crops depleted soil water in a dry year (2019–2020), but to a less extent in a wet year (2018–2019). In either year, however, corn yield was not reduced in association with cover crop use, although the improved shoot biomass growth in corn associated with mustard cover crops was observed in the wet year but not in the dry year. Mustard cover crops tended to reduce deep drainage during the corn seasons, which has implications in preventing the leaching loss of nitrogen in the crop root zone.
DOI: 10.6084/m9.figshare.20770835
title: The combination of vermicompost and arbuscular mycorrhizal fungi improves the physiological properties and chemical composition of <i>Opuntia ficus-indica</i> under semi-arid conditions in the field

description: Drought is one of the major threats to food security in arid and semi-arid regions. Therefore, significant changes in agricultural production systems will be required to meet the challenges of food security while addressing water scarcity. Prickly pear is a drought tolerant plant, as well as a source of sustainable food and feed. Nonetheless, in dry conditions, its growth and performance are restricted. The aim of this study was to evaluate the effect of arbuscular mycorrhizal fungi (AMF), vermicompost (Vc) or the combination of AMF + Vc on yield, growth and physio-chemical parameters of cactus grown under field drought conditions. Two irrigation regimes were applied, non-irrigated (grown under rainfed conditions) and irrigated plants (8 mm of water per week). After eight months of cultivation, the finding demonstrated that drought reduced growth, physiological and biochemical parameters of cactus. However, the application of biostimulants, especially Vc and AMF + Vc, can mitigate the negative effect of drought by increasing cladode dry weight (93% and 109%), total chlorophyll (78% and 75%), total phenolic content (83% and 81%). Those treatments are also efficient in enhancing activities of enzymatic and non enzymatic antioxidants in cactus cladodes and fruits. These results suggest that the use of these biostimulants can mitigate the challenges associated with drought, by improving the physiological and biochemical responses of cactus.
DOI: 10.6084/m9.figshare.20770835.v2
title: The combination of vermicompost and arbuscular mycorrhizal fungi improves the physiological properties and chemical composition of <i>Opuntia ficus-indica</i> under semi-arid conditions in the field

description: Drought is one of the major threats to food security in arid and semi-arid regions. Therefore, significant changes in agricultural production systems will be required to meet the challenges of food security while addressing water scarcity. Prickly pear is a drought tolerant plant, as well as a source of sustainable food and feed. Nonetheless, in dry conditions, its growth and performance are restricted. The aim of this study was to evaluate the effect of arbuscular mycorrhizal fungi (AMF), vermicompost (Vc) or the combination of AMF + Vc on yield, growth and physio-chemical parameters of cactus grown under field drought conditions. Two irrigation regimes were applied, non-irrigated (grown under rainfed conditions) and irrigated plants (8 mm of water per week). After eight months of cultivation, the finding demonstrated that drought reduced growth, physiological and biochemical parameters of cactus. However, the application of biostimulants, especially Vc and AMF + Vc, can mitigate the negative effect of drought by increasing cladode dry weight (93% and 109%), total chlorophyll (78% and 75%), total phenolic content (83% and 81%). Those treatments are also efficient in enhancing activities of enzymatic and non enzymatic antioxidants in cactus cladodes and fruits. These results suggest that the use of these biostimulants can mitigate the challenges associated with drought, by improving the physiological and biochemical responses of cactus.
DOI: 10.5281/zenodo.5639495
title: Digital replica of the Tomb of Reliefs at Cerveteri

description: Survey and creation of a digital replica of the interior of the Tomb of Reliefs located in the Banditaccia Necropolis in Cerveteri (RM). It is the only Etruscan tomb (4th BC) decorated with stucco reliefs, unusual compared to the usual frescoes. The dataset, because of its high resolution and accuracy, is a useful tool for study, restoration planning and enhancement of an environment normally closed to the public for conservation reasons. The dataset was acquired with active (Faro laser scanner) and passive (full-frame SLR) sensors through a spherical photogrammetry campaign. The data were reprocessed by combining Structure from Motion techniques to obtain a photogrammetric solution and Computer Graphic for colour correction (with digital painting tools) and geometry and texture optimization. The data mainly concern the 3D domain, have been reprocessed primarily with open source software and are stored in open formats: photogrammetric solution in utf-8 txt files, point clouds in binary ply, polygon meshes with mapping coordinates in blend format, images in jpeg format. The working group consists of researchers from CNR-ISPC: Enzo d'Annibale, Emanuel Demetrescu, Daniele Ferdani.
DOI: 10.6084/m9.figshare.21995069.v2
title: Files for Main Figure 4

description: 6 Cell lines TE matrices quantified by long-read, Telescope(short-read), lasTEq(short-read). Used for main figure 4 <br> 1. SG-Nex_A549: TE counts by long-read, Telescope(short-read), lasTEq(short-read) using A549 cell line in SG-NEx study 2. SG-Nex_HepG2: TE counts by long-read, Telescope(short-read), lasTEq(short-read) using HepG2 cell line in SG-NEx study 3. SG-Nex_HCT116: TE counts by long-read, Telescope(short-read), lasTEq(short-read) using HCT116 cell line in SG-NEx study 4. SG-Nex_K562: TE counts by long-read, Telescope(short-read), lasTEq(short-read) using K562 cell line in SG-NEx study 5. SG-Nex_MCF-7: TE counts by long-read, Telescope(short-read), lasTEq(short-read) using MCF-7 cell line in SG-NEx study 6. ownHCT116: TE counts by long-read, Telescope(short-read), lasTEq(short-read) using HCT116 sample generated by our lab
DOI: 10.6084/m9.figshare.22139921
title: RSI-CB256

description: RSI-CB256 has more than 24,000 images and 35 categories with 690 images per category. RSI-CB has a higher spatial resolution than other existing datasets, which can be seen clearly from the image memory size. <br>
DOI: 10.6084/m9.figshare.22139994
title: Section_4_two_particle_vertical from Effect of defects and reinforcements on the mechanical behaviour of a bi-layered panel

description: Dataset for figures in section 4 for two top-down particle case
DOI: 10.6084/m9.figshare.22139994.v1
title: Section_4_two_particle_vertical from Effect of defects and reinforcements on the mechanical behaviour of a bi-layered panel

description: Dataset for figures in section 4 for two top-down particle case
DOI: 10.6084/m9.figshare.22139997
title: Section 5_figures from Effect of defects and reinforcements on the mechanical behaviour of a bi-layered panel

description: Dataset for figures in section 5
DOI: 10.6084/m9.figshare.22139997.v1
title: Section 5_figures from Effect of defects and reinforcements on the mechanical behaviour of a bi-layered panel

description: Dataset for figures in section 5
DOI: 10.6084/m9.figshare.22140003
title: Section_4_two_particle_Horizon.opju from Effect of defects and reinforcements on the mechanical behaviour of a bi-layered panel

description: Dataset for figures in section 4 for two side-by-side particle case
DOI: 10.6084/m9.figshare.22140003.v1
title: Section_4_two_particle_Horizon.opju from Effect of defects and reinforcements on the mechanical behaviour of a bi-layered panel

description: Dataset for figures in section 4 for two side-by-side particle case
DOI: 10.6084/m9.figshare.22140006
title: Section 4_one_particle_figures.opju from Effect of defects and reinforcements on the mechanical behaviour of a bi-layered panel

description: Dataset for figures in section 4 for single particle case
DOI: 10.6084/m9.figshare.22140006.v1
title: Section 4_one_particle_figures.opju from Effect of defects and reinforcements on the mechanical behaviour of a bi-layered panel

description: Dataset for figures in section 4 for single particle case
DOI: 10.5281/zenodo.7464484
title: Metastability as a neuromechanistic biomarker of schizophrenia pathology

description: Matlab files for Human Connectome Project - Early Psychosis (HCPEP) and COBRE in AAL116 parcellation. HCPEP files contain data for 4 runs of resting-state fMRI for healthy controls and non-affective psychosis groups. COBRE files contain data for 1 run of resting-state fMRI for healthy controls and established schizophrenia groups.
description: {"references": ["Hancock et al., (2022) - Matlab files for https://www.medrxiv.org/content/10.1101/2022.10.14.22281093v1"]}
DOI: 10.5281/zenodo.7464483
title: Metastability as a neuromechanistic biomarker of schizophrenia pathology

description: Matlab files for Human Connectome Project - Early Psychosis (HCPEP) and COBRE in AAL116 parcellation. HCPEP files contain data for 4 runs of resting-state fMRI for healthy controls and non-affective psychosis groups. COBRE files contain data for 1 run of resting-state fMRI for healthy controls and established schizophrenia groups.
description: {"references": ["Hancock et al., (2022) - Matlab files for https://www.medrxiv.org/content/10.1101/2022.10.14.22281093v1"]}
DOI: 10.6084/m9.figshare.22133015
title: Kuppe snRNA-seq Human Heart 2022 control

description: Dataset published by Kuppe et al. 2022, which contains data from human cardiac remodelling after myocardial infarction using single-cell gene expression, chromatin accessibility and spatial transcriptomic profiling of multiple physiological zones in myocardium from patients with myocardial infarction and controls. <br> The dataset available under this link contains the single-cell gene expression part from all control patients. <strong>Citation</strong> Kuppe, C., Ramirez Flores, R.O., Li, Z. <em>et al.</em> Spatial multi-omic map of human myocardial infarction. <em>Nature</em> <strong>608</strong>, 766–777 (2022). <strong>Manuscript link</strong> https://www.nature.com/articles/s41586-022-05060-x <strong>Original data link</strong> https://cellxgene.cziscience.com/collections/8191c283-0816-424b-9b61-c3e1d6258a77
DOI: 10.6084/m9.figshare.22133015.v1
title: Kuppe snRNA Human Heart 2022 control

description: Dataset published by Kuppe et al. 2022, which contains data from human cardiac remodelling after myocardial infarction using single-cell gene expression, chromatin accessibility and spatial transcriptomic profiling of multiple physiological zones in myocardium from patients with myocardial infarction and controls. <br> The dataset available under this link contains the single-cell gene expression part from all control patients. <strong>Citation</strong> Kuppe, C., Ramirez Flores, R.O., Li, Z. <em>et al.</em> Spatial multi-omic map of human myocardial infarction. <em>Nature</em> <strong>608</strong>, 766–777 (2022). <strong>Manuscript link</strong> https://www.nature.com/articles/s41586-022-05060-x <strong>Original data link</strong> https://cellxgene.cziscience.com/collections/8191c283-0816-424b-9b61-c3e1d6258a77
DOI: 10.5281/zenodo.7663956
title: Datasets for article Effect of disease prevalence and growth stage on symptoms severity in the Turnip mosaic virus - Arabidopsis thaliana pathosystem

description: Plants generate volatile organic compounds (VOCs) in response to biotic and abiotic stimuli that provide information about the physiological status of emitters to other individuals in the community. Nearby receivers adjust their own defenses in response to these chemical cues. The majority of studies to date has concentrated on the communication of abiotic stressors (<em>e.g</em>. salinity or drought) or herbivory. Less attention had received the role of VOCs during microbial infections and almost nothing has been done for viruses. Here we investigated the function of VOCs during turnip mosaic virus infection of <em>Arabidopsis thaliana</em>. First, we looked at the influence of two factors on the kinetics of symptoms progression in receivers, namely the prevalence of infection in the population and the growth stage of the receiver plants at inoculation. We found that young plants were more sensitive to the protective effect of VOCs than older ones, and that high infection prevalence results in a slower disease progression in receivers. Second, we looked into the possibility that jasmonates could be VOC candidates. To do this, we examined the kinetics of symptoms progression in jasmonate-insensitive and wild-type plants, and the results showed that the protective effect vanished in the mutant plants. Third, we investigated the possibility that root communication would be also relevant. Our findings showed that the kinetics of symptom progression across receivers was further slowed down when plants were housed in the same pot. Together, our preliminary findings point to a potential function for disease prevalence in plant communities in regulating the severity of symptoms, this effect being mediated by VOCs.
DOI: 10.5281/zenodo.7663955
title: Datasets for article Effect of disease prevalence and growth stage on symptoms severity in the Turnip mosaic virus - Arabidopsis thaliana pathosystem

description: Plants generate volatile organic compounds (VOCs) in response to biotic and abiotic stimuli that provide information about the physiological status of emitters to other individuals in the community. Nearby receivers adjust their own defenses in response to these chemical cues. The majority of studies to date has concentrated on the communication of abiotic stressors (<em>e.g</em>. salinity or drought) or herbivory. Less attention had received the role of VOCs during microbial infections and almost nothing has been done for viruses. Here we investigated the function of VOCs during turnip mosaic virus infection of <em>Arabidopsis thaliana</em>. First, we looked at the influence of two factors on the kinetics of symptoms progression in receivers, namely the prevalence of infection in the population and the growth stage of the receiver plants at inoculation. We found that young plants were more sensitive to the protective effect of VOCs than older ones, and that high infection prevalence results in a slower disease progression in receivers. Second, we looked into the possibility that jasmonates could be VOC candidates. To do this, we examined the kinetics of symptoms progression in jasmonate-insensitive and wild-type plants, and the results showed that the protective effect vanished in the mutant plants. Third, we investigated the possibility that root communication would be also relevant. Our findings showed that the kinetics of symptom progression across receivers was further slowed down when plants were housed in the same pot. Together, our preliminary findings point to a potential function for disease prevalence in plant communities in regulating the severity of symptoms, this effect being mediated by VOCs.
DOI: 10.25345/c54j0b70j
title: MassIVE MSV000091342 - GPX4 immunoprecipitation in Huh7 cells
title: Huh7 cells with expression of Flag-GPX4 were treated with IGF1. An immunoprecipitation assay was performed, and immunoprecipitates were subjected to masspec analysis.
DOI: 10.6084/m9.figshare.22140060
title: Langwig WNS fat Supplement from Shifting effects of host physiological condition following pathogen establishment

description: Supplemental tables and figures
DOI: 10.18112/openneuro.ds004509.v1.0.0
title: Extensive topographic remapping and functional sharpening in the adult rat visual pathway upon first visual experience
DOI: 10.25392/leicester.data.20391477
title: Monoamine Neuromodulation is a Bilaterian Innovation Results

description: Results of the phylogenomic analyses of Monoamine pathway genes. Including phylogenetic trees, orthogroup selection, species tree-gene tree reconciliation. <br> Results were produced as part of the paper Goulty et al, 2022, Monoamine Neuromodulation is a Bilaterian Innovation.
DOI: 10.25392/leicester.data.20391477.v2
title: Monoamine Neuromodulation is a Bilaterian Innovation Results

description: Results of the phylogenomic analyses of Monoamine pathway genes. Including phylogenetic trees, orthogroup selection, species tree-gene tree reconciliation. <br> Results were produced as part of the paper Goulty et al, 2022, Monoamine Neuromodulation is a Bilaterian Innovation.
DOI: 10.25392/leicester.data.20391477.v1
title: Monoamine Neuromodulation is a Bilaterian Innovation Results

description: Results of the phylogenomic analyses of Monoamine pathway genes. Including phylogenetic trees, orthogroup selection, species tree-gene tree reconciliation. <br> Results were produced as part of the paper Goulty et al, 2022, Monoamine Neuromodulation is a Bilaterian Innovation.
DOI: 10.21335/nmdc-1313521943
title: Environmental DNA OOE Cruise 2021051 – Investigating Ocean diversity and climate impact through quantitative assessment of selected marine taxonomic groups

description: Molecular biology methods, such as environmental DNA (eDNA)analysis, are the new frontier in biodiversity assessments. Understanding the status of ocean biodiversity and impact of climate change on the composition, structure and function of marine ecosystems is crucial to sustainable management of the ocean and coastal areas. Within the eDNA activity on board of the One Ocean Expedition (OOE), a total of 240 water samples will be collected and 60 of them will be analyzed onsite using a portable PCR device. Weekly analysis of eDNA will provide hundreds of data points around the globe to assess the presence and abundance of 11 key marine indicators from marine unicellular prokaryotes to fish that may be impacted in one way or another by ocean and climate change. The geographical mapping of these species across all oceanic regions of the globe will provide new knowledge, status, and insights into how species may redistribute in a changing ocean resulting from global warning and other anthropogenic stressors. The rest of the collected samples will be analyzed with higher resolution using high-throughput sequencing (HTS) techniques to infer marine species inventory and biodiversity distribution at a scale seldom possible in scientific cruises, providing a snapshot of marine biodiversity globally.
The results provided in the datasets are automatically tagged with a quality flag according to SeaDataNet standards:
https://www.seadatanet.org/content/download/596/file/SeaDataNet_QC_procedures_V2_%28May_2010%29.pdf

QC = 0 - no quality check QC = 1 - good QC = 2 - probably_good QC = 3 - probably_bad

Quality = 2 was assigned if the assay was not valid but there was valid replication in one (out of possible 3) PCR results.

Quality = 3 was assigned if the melting point lies outside of the required range. In this case the abundance is set to zero.
DOI: 10.21335/nmdc-1310495588
title: Environmental DNA OOE Cruise 2021052 – Investigating Ocean diversity and climate impact through quantitative assessment of selected marine taxonomic groups

description: Molecular biology methods, such as environmental DNA (eDNA)analysis, are the new frontier in biodiversity assessments. Understanding the status of ocean biodiversity and impact of climate change on the composition, structure and function of marine ecosystems is crucial to sustainable management of the ocean and coastal areas. Within the eDNA activity on board of the One Ocean Expedition (OOE), a total of 240 water samples will be collected and 60 of them will be analyzed onsite using a portable PCR device. Weekly analysis of eDNA will provide hundreds of data points around the globe to assess the presence and abundance of 11 key marine indicators from marine unicellular prokaryotes to fish that may be impacted in one way or another by ocean and climate change. The geographical mapping of these species across all oceanic regions of the globe will provide new knowledge, status, and insights into how species may redistribute in a changing ocean resulting from global warning and other anthropogenic stressors. The rest of the collected samples will be analyzed with higher resolution using high-throughput sequencing (HTS) techniques to infer marine species inventory and biodiversity distribution at a scale seldom possible in scientific cruises, providing a snapshot of marine biodiversity globally.
The results provided in the datasets are automatically tagged with a quality flag according to SeaDataNet standards:
https://www.seadatanet.org/content/download/596/file/SeaDataNet_QC_procedures_V2_%28May_2010%29.pdf

QC = 0 - no quality check QC = 1 - good QC = 2 - probably_good QC = 3 - probably_bad

Quality = 2 was assigned if the assay was not valid but there was valid replication in one (out of possible 3) PCR results.

Quality = 3 was assigned if the melting point lies outside of the required range. In this case the abundance is set to zero.
DOI: 10.25326/359
title: METEO-FRANCE, RADAR Double-Polar Radial raw Data from PAM* products

description: NETCDF product with radial grid of resolution 0.5°x1066x240m, available for the double polar radars of the METEO-FRANCE network.<br/>It contains the raw data of the parameters Horizontal Reflectivity, Rhohv, Zdr et Phidp for the antenna rotations of a 15min cycle, in [CF/Radial-1.4](https://permalink.aeris-data.fr/radarsmf_cfradial1-4) standard format.<br/>See [french detailed description](https://permalink.aeris-data.fr/radarsmf_doc_radial_products_fr).
DOI: 10.25326/358
title: METEO-FRANCE, RADAR Simple-Polar Radial raw Data from PAG* Odyssey products

description: NETCDF product with radial grid of resolution 0.5°x256x1000m, available for all the radars of the METEO-FRANCE network.<br/>It contains the raw data of the parameters Horizontal Reflectivity, Sigma and Radial Velocity for the antenna rotations of a 15min cycle, in [CF/Radial-1.4](https://permalink.aeris-data.fr/radarsmf_cfradial1-4) standard format.<br/>See [french detailed description](https://permalink.aeris-data.fr/radarsmf_doc_radial_products_fr).
DOI: 10.25345/c50r9md67
title: MassIVE MSV000091343 - GPX4 immunoprecipitation in Huh7 cells
title: Huh7 cells with expression of Flag-GPX4 were treated with IGF1. An immunoprecipitation assay was performed, and immunoprecipitates were subjected to masspec analysis.
DOI: 10.6084/m9.figshare.22140080
title: GOATS.rar

description: Raw data of INHA gene polymorphism in Hainan black goats
DOI: 10.6084/m9.figshare.22140080.v1
title: GOATS.rar

description: Raw data of INHA gene polymorphism in Hainan black goats