cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.4922038
title: Adenosine derived from CD39-expressing B cells promotes dysregulation of immune responses after sepsis [Scripts]

description: <strong>Summary methodology:</strong><br> <br> We re-analyzed single-cell transcriptomic data from the peripheral blood mononuclear cells (PBMC) of septic patients from a public dataset (Reyes et al., 2020). Basically, the samples were combined into two major groups for further comparisons, septic patients (sepsis) and non-septic patients (no sepsis). The sepsis group included samples from patients with urosepsis and patients with sepsis admitted to the medical intensive care unit, whereas the no sepsis group included samples from healthy patients and patients without sepsis admitted to the medical intensive care unit. B cells were filtered based on the authors' previous annotation for downstream analysis (Reyes et al., 2020). Specifically, the data matrices of 7970 B cells were imported to Seurat v3.1 (Stuart et al., 2019) by filtering genes expressed in at least 10 cells and more than 100 unique molecular identifiers (UMI) counts per cell. For the pre-processing step, outlier cells were filtered out based on three metrics (library size &lt; 10000, number of expressed genes between 200 and 2000, and mitochondrial percentage expression &lt; 5) resulting in a matrix with 13077 genes and 5104 cells. The remaining counts were normalized using the ‘LogNormalize’ method with a scale factor of 10000. The top 2,000 variable genes were then identified using the ‘vst’ method using the FindVariableFeatures function. Percent of mitochondrial genes was regressed out in the scaling step and Principal Component Analysis (PCA) was performed using the top 2,000 variable genes with 50 dimensions. Then, a dimensionality reduction method (UMAP) was performed on the top 7 PCAs. Additionally, a clustering analysis was performed on the first 7 principal components using a resolution of 0.6 followed by a dimensionality reduction method (UMAP). Then, differential gene expression analysis was performed using FindAllMarkers function to obtain a list of significant gene markers for each cluster of cells with default parameters. The plasmablast were identified by expression of CD39 gene count &gt; 0 in the RNA essay (CD39) and BS3 plamablast’s markers previously described by Reyes et al. 2020. For enrichment analyses, we utilized the EnrichR tool (Chen et al., 2013) with the Reactome 2016 database for gene markers of plasmablasts.<br> <br> <br> Here we provide R scripts utilized for single cell data analysis of B cell subpopulations: b_cells_sepsis_processing.R : Script to process the B cell population. SEP_Bcells_sel.rds : RDS file generated by script b_cells_sepsis_processing.R count_cell_frequencies_expressing_cd39.R: Script to count cell frequencies in cd39+ clusters.
DOI: 10.5281/zenodo.4922037
title: Adenosine derived from CD39-expressing B cells promotes dysregulation of immune responses after sepsis [Scripts]

description: <strong>Summary methodology:</strong><br> <br> We re-analyzed single-cell transcriptomic data from the peripheral blood mononuclear cells (PBMC) of septic patients from a public dataset (Reyes et al., 2020). Basically, the samples were combined into two major groups for further comparisons, septic patients (sepsis) and non-septic patients (no sepsis). The sepsis group included samples from patients with urosepsis and patients with sepsis admitted to the medical intensive care unit, whereas the no sepsis group included samples from healthy patients and patients without sepsis admitted to the medical intensive care unit. B cells were filtered based on the authors' previous annotation for downstream analysis (Reyes et al., 2020). Specifically, the data matrices of 7970 B cells were imported to Seurat v3.1 (Stuart et al., 2019) by filtering genes expressed in at least 10 cells and more than 100 unique molecular identifiers (UMI) counts per cell. For the pre-processing step, outlier cells were filtered out based on three metrics (library size &lt; 10000, number of expressed genes between 200 and 2000, and mitochondrial percentage expression &lt; 5) resulting in a matrix with 13077 genes and 5104 cells. The remaining counts were normalized using the ‘LogNormalize’ method with a scale factor of 10000. The top 2,000 variable genes were then identified using the ‘vst’ method using the FindVariableFeatures function. Percent of mitochondrial genes was regressed out in the scaling step and Principal Component Analysis (PCA) was performed using the top 2,000 variable genes with 50 dimensions. Then, a dimensionality reduction method (UMAP) was performed on the top 7 PCAs. Additionally, a clustering analysis was performed on the first 7 principal components using a resolution of 0.6 followed by a dimensionality reduction method (UMAP). Then, differential gene expression analysis was performed using FindAllMarkers function to obtain a list of significant gene markers for each cluster of cells with default parameters. The plasmablast were identified by expression of CD39 gene count &gt; 0 in the RNA essay (CD39) and BS3 plamablast’s markers previously described by Reyes et al. 2020. For enrichment analyses, we utilized the EnrichR tool (Chen et al., 2013) with the Reactome 2016 database for gene markers of plasmablasts.<br> <br> <br> Here we provide R scripts utilized for single cell data analysis of B cell subpopulations: b_cells_sepsis_processing.R : Script to process the B cell population. SEP_Bcells_sel.rds : RDS file generated by script b_cells_sepsis_processing.R count_cell_frequencies_expressing_cd39.R: Script to count cell frequencies in cd39+ clusters.
DOI: 10.6073/pasta/0a3d1d6e148241291b5a8f54ebdadd3b
title: Soil Respiration, Temperature and Moisture at Harvard Forest EMS Tower 1995-2014

description: We have been making long-term soil respiration measurements at our transect sites since the summer of 1995. The rainfall exclusion experiment began in May of 2001 and autochamber measurements began in 2003. A root exclusion experiment (trenching) was conducted from 2012-2014.
DOI: 10.25934/00006865.1
title: Available IPD datapackage for study 'Treatment in Patients With Suspected or Confirmed COVID-19 With Early Moderate or Severe Disease: A Randomized Clinical Trial'

description: Vivli is an independent, non-profit organization that has developed a global data-sharing and analytics platform to serve all elements of the international research community. Our mission is to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through the creation and implementation of a sustainable global data-sharing enterprise. The Vivli platform includes an independent data repository, in-depth search engine and a cloud-based, secure analytics platform.
DOI: 10.6084/m9.figshare.14763240.v1
title: HDACi protects against vascular cognitive impairment from CCH injury via induction of BDNF-related AMPA receptor activation

description: HDACi protects against vascular cognitive impairment from CCH injury via induction of BDNF-related AMPA receptor activation
DOI: 10.6084/m9.figshare.14763240
title: HDACi protects against vascular cognitive impairment from CCH injury via induction of BDNF-related AMPA receptor activation

description: HDACi protects against vascular cognitive impairment from CCH injury via induction of BDNF-related AMPA receptor activation
DOI: 10.5281/zenodo.4870493
title: Data of the study Host age and surrounding vegetation affect the community and colonisation rates of arbuscular mycorrhizal fungi in a temperate grassland

description: This dataset supplements our paper published in New Phytologist, in which we ask following questions: What effects does the ontogenetic stage of host plants have and do these effects differ between plant functional groups? Are the AMF communities modified by the properties of surrounding vegetation, such as the proportion of different functional groups or non-mycorrhizal plants? We addressed these questions in a temperate grassland and studied AMF communities using next-generation sequencing and light microscopy, evaluating their composition, taxonomic, phylogenetic and functional diversity, functional traits, and root colonisation levels. We found important differences of AMF communities and their diversity between seedlings and adults, larger than the differences among host species or between functional groups. The proportion of non-mycorrhizal plants in the surrounding affected AMF community composition and increased its richness. Our results highlight the need for further investigating the existence of a common mycelial networks. The decision to use seedlings for experimental work can affect the results more than the chosen host species.
description: The first sheet, called Metadata, describes the contents of the other sheets.
DOI: 10.6084/m9.figshare.14762967
title: Appendices and Supplementary Material of Beutel et al., Patterns of morphological simplification and innovation in the megadiverse Holometabola (Insecta). Cladistics.

description: Appendices:I. Characters used in the analyses. II Apomorphies of Holometabola and its subgrous. III. References cited in appendices I and II.IV. Topology used for reconstruction of character evolution.Supplementary Data:<br>Data matrix (WinClada and NEXUS files).Visualisation of character evolution reconstructed for each character using maximum likelihood (ZIP-file).
DOI: 10.25934/00006627.1
title: Available IPD datapackage for study 'Treating COVID-19 With Hydroxychloroquine: A Multicenter Randomized, Double-blind, Placebo-controlled Clinical Trial in Hospitalized Adults'

description: Vivli is an independent, non-profit organization that has developed a global data-sharing and analytics platform to serve all elements of the international research community. Our mission is to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through the creation and implementation of a sustainable global data-sharing enterprise. The Vivli platform includes an independent data repository, in-depth search engine and a cloud-based, secure analytics platform.
DOI: 10.25934/00006752.0
title: Available IPD datapackage for study 'Oxygen-Ozone as Adjuvant Treatment in Early Control of Disease Progression in Patients With COVID-19 Associated With Modulation of the Gut Microbial Flora'

description: Vivli is an independent, non-profit organization that has developed a global data-sharing and analytics platform to serve all elements of the international research community. Our mission is to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through the creation and implementation of a sustainable global data-sharing enterprise. The Vivli platform includes an independent data repository, in-depth search engine and a cloud-based, secure analytics platform.
DOI: 10.25934/00006595.1
title: Available IPD datapackage for study 'A Randomized, Controlled Clinical Trial of the Safety and Efficacy of Hydroxychloroquine for the Treatment of COVID-19 in Hospitalized Patients'

description: Vivli is an independent, non-profit organization that has developed a global data-sharing and analytics platform to serve all elements of the international research community. Our mission is to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through the creation and implementation of a sustainable global data-sharing enterprise. The Vivli platform includes an independent data repository, in-depth search engine and a cloud-based, secure analytics platform.
DOI: 10.25934/00006713.1
title: Available IPD datapackage for study 'WU 352: Open-label, Randomized Controlled Trial of Hydroxychloroquine Alone or Hydroxychloroquine Plus Azithromycin or Chloroquine Alone or Chloroquine Plus Azithromycin in the Treatment of SARS CoV-2 Infection'

description: Vivli is an independent, non-profit organization that has developed a global data-sharing and analytics platform to serve all elements of the international research community. Our mission is to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through the creation and implementation of a sustainable global data-sharing enterprise. The Vivli platform includes an independent data repository, in-depth search engine and a cloud-based, secure analytics platform.
DOI: 10.5517/ccdc.csd.cc234y4c
title: CCDC 1941162: Experimental Crystal Structure Determination

description: Related Article: Byung Hak Jhun, Dong Yeun Jeong, Sanghee Nah, Soo Young Park, Youngmin You|2021|J.Mater.Chem.C|9|7083|doi:10.1039/D1TC00660F
DOI: 10.5517/ccdc.csd.cc2788ld
title: CCDC 2063533: Experimental Crystal Structure Determination

description: Related Article: Sergio Rodriguez-Arévalo, Andrea Bagán, Christian Griñán-Ferré, Foteini Vasilopoulou, Mercè Pallàs, Iria Brocos-Mosquera, Luis F. Callado, M. Isabel Loza, Antón L. Martínez, José Brea, Belén Pérez, Elies Molins, Steven De Jonghe, Dirk Daelemans, Milica Radan, Teodora Djikic, Katarina Nikolic, Elena Hernández-Hernández, M. Julia García-Fuster, Jesús A. García-Sevilla, Carmen Escolano|2021|Eur.J.Med.Chem.|222|113540|doi:10.1016/j.ejmech.2021.113540
DOI: 10.5517/ccdc.csd.cc279lms
title: CCDC 2064805: Experimental Crystal Structure Determination

description: Related Article: Manpreet Singh, Athulya S. Palakkal, Renjith S. Pillai, Subhadip Neogi|2021|J.Mater.Chem.C|9|7142|doi:10.1039/D1TC01123E
DOI: 10.5517/ccdc.csd.cc279lnt
title: CCDC 2064806: Experimental Crystal Structure Determination

description: Related Article: Manpreet Singh, Athulya S. Palakkal, Renjith S. Pillai, Subhadip Neogi|2021|J.Mater.Chem.C|9|7142|doi:10.1039/D1TC01123E
DOI: 10.5517/ccdc.csd.cc27dmkv
title: CCDC 2067717: Experimental Crystal Structure Determination

description: Related Article: Biao Yang, Han Wu, Liang Zhao|2021|Chem.Commun.|57|5770|doi:10.1039/D1CC01162F
DOI: 10.5517/ccdc.csd.cc27dmlw
title: CCDC 2067718: Experimental Crystal Structure Determination

description: Related Article: Biao Yang, Han Wu, Liang Zhao|2021|Chem.Commun.|57|5770|doi:10.1039/D1CC01162F
DOI: 10.5517/ccdc.csd.cc27hm5k
title: CCDC 2070588: Experimental Crystal Structure Determination

description: Related Article: Sofya S. Kuvshinova, Yulia V. Nelyubina, Vladimir A. Larionov, Daria V. Vorobyeva, Sergey N. Osipov, Dsmitry A. Loginov|2021|J.Organomet.Chem.|946-947|121899|doi:10.1016/j.jorganchem.2021.121899
DOI: 10.5517/ccdc.csd.cc27p58d
title: CCDC 2075923: Experimental Crystal Structure Determination

description: Related Article: Yali Wang, Haiyan Jiang, Xueling Liu, Jun Xu, Yan Gao, Nathaniel S. Finney|2021|Chem.Commun.|57|5818|doi:10.1039/D1CC02307A
DOI: 10.5517/ccdc.csd.cc27p59f
title: CCDC 2075924: Experimental Crystal Structure Determination

description: Related Article: Yali Wang, Haiyan Jiang, Xueling Liu, Jun Xu, Yan Gao, Nathaniel S. Finney|2021|Chem.Commun.|57|5818|doi:10.1039/D1CC02307A
DOI: 10.5517/ccdc.csd.cc27msj6
title: CCDC 2074598: Experimental Crystal Structure Determination

description: Related Article: Samrat Kundu, Ankush Banerjee, Shyam Chand Pal, Meghna Ghosh, Modhu Sudan Maji|2021|Chem.Commun.|57|5762|doi:10.1039/D1CC00668A
DOI: 10.5517/ccdc.csd.cc27rp3t
title: CCDC 2078336: Experimental Crystal Structure Determination

description: Related Article: Samrat Kundu, Ankush Banerjee, Shyam Chand Pal, Meghna Ghosh, Modhu Sudan Maji|2021|Chem.Commun.|57|5762|doi:10.1039/D1CC00668A
DOI: 10.5517/ccdc.csd.cc27rp4v
title: CCDC 2078337: Experimental Crystal Structure Determination

description: Related Article: Samrat Kundu, Ankush Banerjee, Shyam Chand Pal, Meghna Ghosh, Modhu Sudan Maji|2021|Chem.Commun.|57|5762|doi:10.1039/D1CC00668A
DOI: 10.25345/c5kn70
title: MassIVE MSV000087602 - Cardiolipin remodeling enables protein crowding in the inner mitochondrial membrane
title: Mitochondrial cristae are more crowded with proteins than other cellular membranes. However, protein crowding stresses the bilayer organization of lipids, which challenges membrane stability. We tested the hypothesis that the high concentration of proteins drives the tafazzin-catalyzed remodeling of fatty acids in cardiolipin (CL) to reduce stress on the lipid bilayer
DOI: 10.6084/m9.figshare.14763315
title: Supplementary Table 1. Performance matrices.docx

description: <b>Table 1. </b>Baseline characteristics of participants in polypectomy follow-up study<b>Table 2. </b>Summary of operational taxonomix units obtained in this study using 16S RNA Sequencing
DOI: 10.6084/m9.figshare.14763315.v1
title: Supplementary Table 1. Performance matrices.docx

description: <b>Table 1. </b>Baseline characteristics of participants in polypectomy follow-up study<b>Table 2. </b>Summary of operational taxonomix units obtained in this study using 16S RNA Sequencing
DOI: 10.25573/data.10068071.v2
title: SST_Bocas Station Platform

description: Sea Surface temperature monitoring at the Bocas del Toro Monitoring platform.<br>Location: 9.35078 -82.25768Depth: 1m<br>
DOI: 10.25573/data.10068098.v1
title: SST_Galeta Reef, Upstream

description: Sea Surface temperature monitoring on the upstream side of the reef in front of the Galeta Station main building<br>Location: 9.40253 -79.86064<br>Depth: 0.5m<br><br>Status: Active<br>
DOI: 10.5281/zenodo.4923010
title: Dataset for gait-based authentication

description: This dataset can be used for identifying and authenticating people according to their way of walking. Information contained in the dataset is especially suitable as train and test data for machine learning models. The data for this dataset has been gathered in a corridor with a RGB (Red, Blue and Green) camera at 30 FPS (Frames Per Second). The dataset is composed by videos of 14 people walking through a 4 meter distance in the most natural way. This dataset contains 10523 JSON files composed by 2D coordinates for each point of the body provided by OpenPose. 14 people were recorded walking These keypoints are: nose, neck, right shoulder, right elbow, right wrist, left shoulder, left elbow, left wrist, right hip, right knee, right ankle, left hip, left knee, left ankle, right eye, left eye, right ear, left ear, left big toe, left small toe, left heel, right big toe, right small toe and right heel. JSON files are named as follows: Subject_XX_YY_ZZZZZZZZZZZZ_keypoints.json XX: Person ID YY: Video ID ZZZZZZZZZZZZ: Frame ID
DOI: 10.25573/data.10068074.v1
title: SST_Bocas, Isla Bastimentos

description: Sea Surface temperature monitoring at Isla Bastamientos in the area of Bocas del Toro.<br>Location: 9.37222 -82.20111Depths: 3m, 9.1m, 18.3m<br>Status: Inactive<br>
DOI: 10.25573/data.10068107.v1
title: SST_Bay of Panama, Isla Pacheca

description: Sea Surface temperature monitoring near Isla Pacheca<br>Location (more exact coordinates available on request):8.66 -79.05<br>Depth: 6m<br><br>Status: Active<br>
DOI: 10.25573/data.10068092.v1
title: SST_Galeta Reef, Downstream

description: Sea Surface temperature monitoring on the downstream side of the reef in front of the Galeta Station main building<br><br>Location: 9.40336 -79.86036<br>Depth: 0.5m<br><br>Status: Active<br>
DOI: 10.25573/data.10068095.v2
title: SST_Galeta Channel

description: Sea Surface temperature monitoring in the outflow channel in front of the Galeta Station pier<br>Location (more exact coordinates available on request): 9.40 -79.85<br>Depth: 3m<br>Status: Active<br>
DOI: 10.6084/m9.figshare.14714166
title: CANode Metagenome Bins

description: Annotated metagenome assembled genome bins from CANode reactors. Genbank files and protein sequences predicted by RAST annotation. Supports the paper "Metagenomic and metatranscriptomic characterization of a microbial community that catalyzes both energy-generating and energy-storing electrode reactions" by Rebecca L. Mickol, Brian J. Eddie, Anthony P. Malanoski, Matthew D. Yates, Leonard M. Tender, and Sarah M. Glaven
DOI: 10.6084/m9.figshare.14714166.v1
title: CANode Metagenome Bins

description: Annotated metagenome assembled genome bins from CANode reactors. Genbank files and protein sequences predicted by RAST annotation. Supports the paper "Metagenomic and metatranscriptomic characterization of a microbial community that catalyzes both energy-generating and energy-storing electrode reactions" by Rebecca L. Mickol, Brian J. Eddie, Anthony P. Malanoski, Matthew D. Yates, Leonard M. Tender, and Sarah M. Glaven
DOI: 10.5281/zenodo.4923751
title: Computed_Embeddings

description: RotatE Embeddings of entities and relations in a large graph infused with knowledge about CoV. 16000 Epochs, gamma=12, batch size=1024, loss=logsigmoid
DOI: 10.25573/data.10068044.v1
title: SST_Bocas, Isla Colon, Seagrass

description: Sea Surface temperature monitoring near Isla Colon in the sea grass bed near to the STRI station<br>Location: 9.35169 -82.25781<br>Depth: 2m<br><br>Status: Active<br>
DOI: 10.5281/zenodo.4923750
title: Computed_Embeddings

description: RotatE Embeddings of entities and relations in a large graph infused with knowledge about CoV. 16000 Epochs, gamma=12, batch size=1024, loss=logsigmoid
DOI: 10.25573/data.10068038.v1
title: SST_Bay of Panama, Isla Taboguilla

description: Sea Surface temperature monitoring near Isla Taboguilla in the Bay of Panama.<br>Location (more exact coordinates available on request): 8.80 -79.52<br>Depth: 12m<br>Status: Active<br>
DOI: 10.25573/data.10068047.v1
title: SST_Bocas, Isla Colon, Mangrove Mud

description: Sea Surface temperature monitoring near to Isla Colon. This sensor is located in a mud flat and intended to measure the surface temperature of the mud.<br>Location: 9.35214 -82.25903<br>Depth: n/a<br>Status: Active<br>
DOI: 10.25573/data.10068020.v1
title: SST_Bocas, Isla Solarte, Pta Hospital

description: Sea Surface temperature monitoring at Punta Hospital, Isla Solarte in the area of Bocas del Toro.<br>Location: 9.33389 -82.21889<br>Depth: 0.9m<br>Status: Inactive<br>
DOI: 10.25573/data.10068059.v1
title: SST_Bocas, Isla Cayo Agua

description: Sea Surface temperature monitoring near Isla Cayo Agua, Bocas del Toro.<br>Location (more exact coordinates available on request): 9.13 -82.04<br>Depth: 5.2m<br>Status: Active<br>
DOI: 10.25573/data.10068035.v1
title: SST_Bocas, Isla Colon

description: Sea Surface temperature monitoring near Isla Colon, Bocas del Toro.<br>Location (more exact coordinates available on request): 9.35 -82.26<br>Depths: 1m, 4.6m, 9.1m, 18.3m<br>Status: Active<br>
DOI: 10.25573/data.10068026.v1
title: SST_Bocas, Isla Roldan

description: Sea Surface temperature monitoring near Isla Roldan in the area of Bocas del Toro.<br>Location (more exact coordinates available on request): 9.22 -82.33<br>Depths: 1m, 4.6m, 9.1m 18.3m<br>Status: 4.6m sensor Active only<br>
DOI: 10.25573/data.10042667.v1
title: SST_Bay of Panama, Isla Pachequilla

description: Sea Surface temperature monitoring near Isla Pachequilla<br>Location (more exact coordinates available on request):8.67 -79.06<br>Depth: 6m<br><br>Status: Active
DOI: 10.5281/zenodo.4923775
title: FAIR dataset nonsense

description: This dataset shows that measuring FAIRness by calculation a score on the basis of metadata and algorithms alone, does not actually make for a meaningful dataset.
DOI: 10.5281/zenodo.4923774
title: FAIR dataset nonsense

description: This dataset shows that measuring FAIRness by calculation a score on the basis of metadata and algorithms alone, does not actually make for a meaningful dataset.
DOI: 10.7284/142001
title: GNSS (Global Navigation Satellite System) data collected during research cruise NBP1303 using a Furuno GP-330B instrument system onboard the platform RV Nathaniel B. Palmer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/142002
title: Gyrocompass data collected during research cruise NBP1303 using a Yokogawa CMZ700B instrument system onboard the platform RV Nathaniel B. Palmer

description: Original (unprocessed) data collected during a Field_expedition