cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12678842
title: Hypoxia_Biomarker_qPCR data.xlsxHypoxia Biomarker qPCR Data (Identification of hypoxia-specific biomarkers in salmonids using RNA-sequencing and validation using high-throughput qPCR)Hypoxia Biomarker qPCR Data: Identification of hypoxia-specific biomarkers in salmonids using RNA-sequencing and validation using high-throughput qPCRSupplemental Figures and Tables: Identification of hypoxia-specific biomarkers in salmonids using RNA-sequencing and validation using high-throughput qPCR

description: Identifying early gene expression responses to hypoxia (i.e., low dissolved oxygen) as a tool to assess the degree of exposure to this stressor is crucial for salmonids, because they are increasingly exposed to hypoxic stress due to anthropogenic habitat change, e.g., global warming, excessive nutrient loading, and persistent algal blooms. Our goal was to discover and validate gill gene expression biomarkers specific to the hypoxia response in salmonids across multi-stressor conditions. Gill tissue was collected from 24 freshwater juvenile Chinook salmon (<i>Oncorhynchus tshawytscha</i>), held in normoxia [dissolved oxygen (DO) &gt; 8 mg L<sup>-1</sup>] and hypoxia (DO = 4‒5 mg L<sup>-1</sup>) in 10 and 18°C temperatures for up to six days. RNA-sequencing (RNA-seq) was then used to discover 240 differentially expressed genes between hypoxic and normoxic conditions, but not affected by temperature. The most significantly differentially expressed genes had functional roles in the cell cycle and suppression of cell proliferation associated with hypoxic conditions. The most significant genes (n = 30) were selected for real-time qPCR assay development. These assays demonstrated a strong correlation (r = 0.88; p &lt; 0.001) between the expression values from RNA-seq and the fold changes from qPCR. Further, qPCR of the 30 candidate hypoxia biomarkers was applied to an additional 322 Chinook salmon exposed to hypoxic and normoxic conditions to reveal the top biomarkers to define hypoxic stress. Multivariate analyses revealed that smolt stage, water salinity, and morbidity status were relevant factors to consider with the expression of these genes in relation to hypoxic stress. These hypoxia candidate genes will be put into application screening Chinook salmon to determine the identity of stressors impacting the fish.
DOI: 10.6084/m9.figshare.12678896.v1
title: JVASP-78296 to JVASP-79040

description: JARVIS-DFT
DOI: 10.6084/m9.figshare.12678899.v1
title: JVASP-79041 to JVASP-79756

description: JARVIS-DFT
DOI: 10.6084/m9.figshare.12678842.v1
title: Hypoxia_Biomarker_qPCR data.xlsx

description: Identifying early gene expression responses to hypoxia (i.e., low dissolved oxygen) as a tool to assess the degree of exposure to this stressor is crucial for salmonids, because they are increasingly exposed to hypoxic stress due to anthropogenic habitat change, e.g., global warming, excessive nutrient loading, and persistent algal blooms. Our goal was to discover and validate gill gene expression biomarkers specific to the hypoxia response in salmonids across multi-stressor conditions. Gill tissue was collected from 24 freshwater juvenile Chinook salmon (<i>Oncorhynchus tshawytscha</i>), held in normoxia [dissolved oxygen (DO) &gt; 8 mg L<sup>-1</sup>] and hypoxia (DO = 4‒5 mg L<sup>-1</sup>) in 10 and 18°C temperatures for up to six days. RNA-sequencing (RNA-seq) was then used to discover 240 differentially expressed genes between hypoxic and normoxic conditions, but not affected by temperature. The most significantly differentially expressed genes had functional roles in the cell cycle and suppression of cell proliferation associated with hypoxic conditions. The most significant genes (n = 30) were selected for real-time qPCR assay development. These assays demonstrated a strong correlation (r = 0.88; p &lt; 0.001) between the expression values from RNA-seq and the fold changes from qPCR. Further, qPCR of the 30 candidate hypoxia biomarkers was applied to an additional 322 Chinook salmon exposed to hypoxic and normoxic conditions to reveal the top biomarkers to define hypoxic stress. Multivariate analyses revealed that smolt stage, water salinity, and morbidity status were relevant factors to consider with the expression of these genes in relation to hypoxic stress. These hypoxia candidate genes will be put into application screening Chinook salmon to determine the identity of stressors impacting the fish.
DOI: 10.6084/m9.figshare.12678839
title: Data File for Who Should Be Behind The Wheel? A Study of Oregon's Measure 88

description: This is the data set to the paper "Who Should Be Behind The Wheel? A Study of Oregon's Measure 88"
DOI: 10.6084/m9.figshare.12678839.v1
title: Data File for Who Should Be Behind The Wheel? A Study of Oregon's Measure 88

description: This is the data set to the paper "Who Should Be Behind The Wheel? A Study of Oregon's Measure 88"
DOI: 10.6084/m9.figshare.12678668
title: JVASP-74760 to JVASP-75837

description: JARVIS-DFT
DOI: 10.6084/m9.figshare.12678671
title: JVASP-75838 to JVASP-78295

description: JARVIS-DFT
DOI: 10.6084/m9.figshare.12678665
title: JVASP-73925 to JVASP-74759

description: JARVIS-DFT
DOI: 10.6084/m9.figshare.12678671.v1
title: JVASP-75838 to JVASP-78295

description: JARVIS-DFT
DOI: 10.6084/m9.figshare.12678554
title: SLA_Oct2014

description: SLA for the BoB in early October 2014
DOI: 10.6084/m9.figshare.12678563
title: AR040-MicroCAT-CTD

description: This dataset provides 12 months worth of MicroCAT-CTD data received at ADEON's 7 bottom-lander collection sites. A readme file is included. Recording dates span November 2018 through November 2019<br>See https://adeon.unh.edu/ for more details.
DOI: 10.6084/m9.figshare.12678668.v1
title: JVASP-74760 to JVASP-75837

description: JARVIS-DFT
DOI: 10.6084/m9.figshare.12678554.v1
title: SLA_Oct2014

description: SLA for the BoB in early October 2014
DOI: 10.6084/m9.figshare.12678665.v1
title: JVASP-73925 to JVASP-74759

description: JARVIS-DFT
DOI: 10.6084/m9.figshare.12678536
title: AR040 Fish Tag Counts

description: The ADEON bottom landers are equipped with Vemco Fish Finders which record the tag number of any tagged fish that passes through its vicinity. The fish counters are co-located with the AZPF instruments. While ADEON has 7 acoustic listening sites, the AZFP's and the fish counters are found only at, VAC, HAT, and JAX locations. To see these locations on a map, visit the ADEON projects website. https://adeon.unh.edu<br>Machine Metadata and Data README files included. Readme file shows start time that is tied to the spreadsheet data.
DOI: 10.6084/m9.figshare.12678536.v1
title: AR040 Fish Tag Counts

description: The ADEON bottom landers are equipped with Vemco Fish Finders which record the tag number of any tagged fish that passes through its vicinity. The fish counters are co-located with the AZPF instruments. While ADEON has 7 acoustic listening sites, the AZFP's and the fish counters are found only at, VAC, HAT, and JAX locations. To see these locations on a map, visit the ADEON projects website. https://adeon.unh.edu<br>Machine Metadata and Data README files included. Readme file shows start time that is tied to the spreadsheet data.
DOI: 10.6084/m9.figshare.12678563.v1
title: AR040-MicroCAT-CTD

description: This dataset provides 12 months worth of MicroCAT-CTD data received at ADEON's 7 bottom-lander collection sites. A readme file is included. Recording dates span November 2018 through November 2019<br>See https://adeon.unh.edu/ for more details.
DOI: 10.6084/m9.figshare.12678563.v3
title: AR040-MicroCAT-CTD

description: This dataset provides 12 months worth of MicroCAT-CTD data received at ADEON's 7 bottom-lander collection sites. A readme file is included. Recording dates span November 2018 through November 2019<br>See https://adeon.unh.edu/ for more details.
DOI: 10.6084/m9.figshare.12678563.v2
title: AR040-MicroCAT-CTD

description: This dataset provides 12 months worth of MicroCAT-CTD data received at ADEON's 7 bottom-lander collection sites. A readme file is included. Recording dates span November 2018 through November 2019<br>See https://adeon.unh.edu/ for more details.
DOI: 10.6084/m9.figshare.12678434
title: Odonata from Chimalapas Uxpanapa region Mexico.xlsx

description: During a collecting trip to five tropical rainforest sites in the Chimalapas-Uxpanaparegion in an altitudinal gradient of 155–499 m a.s.l., a total of sixteen species of odonatesnew to the region were recorded. Poorly studied species such as Erpetogomphus ophibolusCalvert, 1905, Hetaerina infecta Calvert, 1901, Heteragrion alienum Williamson, 1919, andHeteragrion tricellulare Calvert, 1901, were recorded. Ischnura demorsa Hagen, 1861, andParaphlebia sp. are discussed in greater detail. These records add to the knowledge of odonatedistribution from Oaxaca and Veracruz.
DOI: 10.6084/m9.figshare.12678434.v1
title: Odonata from Chimalapas Uxpanapa region Mexico.xlsx

description: During a collecting trip to five tropical rainforest sites in the Chimalapas-Uxpanaparegion in an altitudinal gradient of 155–499 m a.s.l., a total of sixteen species of odonatesnew to the region were recorded. Poorly studied species such as Erpetogomphus ophibolusCalvert, 1905, Hetaerina infecta Calvert, 1901, Heteragrion alienum Williamson, 1919, andHeteragrion tricellulare Calvert, 1901, were recorded. Ischnura demorsa Hagen, 1861, andParaphlebia sp. are discussed in greater detail. These records add to the knowledge of odonatedistribution from Oaxaca and Veracruz.
DOI: 10.6084/m9.figshare.12676739
title: Transposon Directed Insertion-site Sequencing of a BW25113 ascA (yecA) deletion mutant

description: We carried out saturated transposon mutagenesis of an <i>ascA</i> deletion mutant, determined the location of the transposon insertions using Illumina sequencing and mapped them to the BW25113 reference genome (CP009273.1). We have deposited three datasets: (1) the number of transposon insertions at each position in the genome (position_depth_count.txt), (2) the number of transposon insertions at each position with the transposon in orientation A (position_depth_count_pos.txt) and (3) the number of transposon insertions at each position with the transposon in orientation B (position_depth_count_neg.txt). <br>
DOI: 10.6084/m9.figshare.12676739.v1
title: Transposon Directed Insertion-site Sequencing of a BW25113 ascA (yecA) deletion mutant

description: We carried out saturated transposon mutagenesis of an <i>ascA</i> deletion mutant, determined the location of the transposon insertions using Illumina sequencing and mapped them to the BW25113 reference genome (CP009273.1). We have deposited three datasets: (1) the number of transposon insertions at each position in the genome (position_depth_count.txt), (2) the number of transposon insertions at each position with the transposon in orientation A (position_depth_count_pos.txt) and (3) the number of transposon insertions at each position with the transposon in orientation B (position_depth_count_neg.txt). <br>
DOI: 10.6084/m9.figshare.12676670
title: Tabla 4: Niveles de la competencia transversal “innovación y resolución de problemas reales” trabajados en las PEA

description: Representa en el los indicadores de la competencia transversal “innovación y resolución de problemas presente en cada una de las PEA
DOI: 10.6084/m9.figshare.12676670.v1
title: Tabla 4: Niveles de la competencia transversal “innovación y resolución de problemas reales” trabajados en las PEA

description: Representa en el los indicadores de la competencia transversal “innovación y resolución de problemas presente en cada una de las PEA
DOI: 10.6084/m9.figshare.12676565
title: Conscious proning _Burton-Papp 2020.numbers

description: This is a data for the use of non invasive ventilation and prone positioning in patients with COVID-19 acute hypoxic respiratory failure. This is a timeline data looking at the oxygenation, heart rate and respiratory rate.
DOI: 10.6084/m9.figshare.12676157
title: Tabla 2: Nivel de apertura de los elementos de diseño PEA (I Iteración)

description: Sintetiza el análisis del nivel de apertura, - bajo (B), medio (M) o alto (A), - siguiendo los parámetros de Ehlers (2010) y Zijdemans (2014) para cada uno de los elementos de diseño en los cuatro escenarios de PEA diseñados. <br>
DOI: 10.6084/m9.figshare.12676421
title: protein clustering of Archaea

description: list of supplementary files
DOI: 10.6084/m9.figshare.12676421.v1
title: protein clustering of Archaea

description: list of supplementary files
DOI: 10.6084/m9.figshare.12676565.v2
title: Conscious proning _Burton-Papp 2020.numbers

description: This is a data for the use of non invasive ventilation and prone positioning in patients with COVID-19 acute hypoxic respiratory failure. This is a timeline data looking at the oxygenation, heart rate and respiratory rate.
DOI: 10.6084/m9.figshare.12676076
title: Hart 2017 Evaluation and Design of Genome-Wide CRISPR/SpCas9 Knockout Screens

description: Data and methods for Hart 2017
DOI: 10.6084/m9.figshare.12676076.v1
title: Hart 2017 Evaluation and Design of Genome-Wide CRISPR/SpCas9 Knockout Screens

description: Data and methods for Hart 2017
DOI: 10.6084/m9.figshare.12676565.v1
title: Conscious proning _Burton-Papp 2020.numbers

description: This is a data for the use of non invasive ventilation and prone positioning in patients with COVID-19 acute hypoxic respiratory failure. This is a timeline data looking at the oxygenation, heart rate and respiratory rate.
DOI: 10.6084/m9.figshare.12675122
title: Flow-based Motion Planner

description: Using flow-based distribution for sampling-based motion planning<br>
DOI: 10.6084/m9.figshare.12675122.v1
title: Flow-based Motion Planner

description: Using flow-based distribution for sampling-based motion planning<br>
DOI: 10.6084/m9.figshare.12674579
title: DESeq2 result file

description: DESeq2 result file from Galaxy.eu
DOI: 10.6084/m9.figshare.12674585
title: dat3_11_18_19.xlsx

description: data on redirection of agression of Vervet Monkeys collected between 2014-2015<br>
DOI: 10.6084/m9.figshare.12674543
title: Salmon quant files

description: Salmon quant data from Galaxy.eu
DOI: 10.6084/m9.figshare.12674585.v1
title: dat3_11_18_19.xlsx

description: data on redirection of agression of Vervet Monkeys collected between 2014-2015<br>
DOI: 10.6084/m9.figshare.12674543.v1
title: Salmon quant files

description: Salmon quant data from Galaxy.eu
DOI: 10.6084/m9.figshare.12674510
title: JVASP-70858 to JVASP-71433

description: JARVIS-DFT
DOI: 10.6084/m9.figshare.12674513
title: JVASP-71434 to JVASP-73922

description: JARVIS-DFT
DOI: 10.6084/m9.figshare.12674525
title: salmonquantS1.tabular

description: salmon quant file from Galaxy.eu
DOI: 10.6084/m9.figshare.12674528
title: Longer photoperiods through range shifts and artificial light lead to a destabilising increase in host-parasitoid interaction strength

description: Main dataset
DOI: 10.6084/m9.figshare.12674513.v1
title: JVASP-71434 to JVASP-73922

description: JARVIS-DFT
DOI: 10.6084/m9.figshare.12674510.v1
title: JVASP-70858 to JVASP-71433

description: JARVIS-DFT
DOI: 10.6084/m9.figshare.12674525.v1
title: salmonquantS1.tabular

description: salmon quant file from Galaxy.eu
DOI: 10.6084/m9.figshare.12674528.v2
title: Longer photoperiods through range shifts and artificial light lead to a destabilising increase in host-parasitoid interaction strength

description: Main dataset
DOI: 10.6084/m9.figshare.12674507
title: JVASP-69752 to JVASP-70857

description: JARVIS-DFT
DOI: 10.6084/m9.figshare.12674528.v1
title: Longer photoperiods through range shifts and artificial light lead to a destabilising increase in host-parasitoid interaction strength

description: Main dataset
DOI: 10.6084/m9.figshare.12674507.v1
title: JVASP-69752 to JVASP-70857

description: JARVIS-DFT
DOI: 10.6084/m9.figshare.12674459
title: Supplementary Material for: Monocyte-Derived Hepatocyte-Like Cell Test: A Novel Tool for in vitro Identification of Drug-Induced Liver Injury in Patients with Herbal or Dietary Supplements

description: <b><i>Background:</i></b> Drug-induced liver injury caused by herbal and dietary supplements (HDS) has been an increasingly important phenomenon in recent years. Diagnosis is the major challenge. Definite causality assessment, especially in patients with concomitant prescription medicine or other potential causes of liver injury, can be impossible. <b><i>Objectives:</i></b> We investigated the usefulness of an in vitro test on the basis of peripheral monocytes of the individual patients in patients with acute liver injury consuming HDS. <b><i>Method:</i></b> Patients with acute liver injury who had been prospectively recruited by the University Hospital Munich (LMU, Munich) and the Chinese University of Hong Kong (CUHK) and who took at least 1 HDS were selected for this analysis. Diagnosis of drug-induced liver injury (DILI) was based on local expert adjudication, Roussel Uclaf Causality Assessment Method (RUCAM) score, and course of the disease and was supported by the monocyte-derived hepatocyte-like (MH) cell test. <b><i>Results:</i></b> We identified 47 patients with liver injury and intake of at least 1 HDS: 32 (68%) were diagnosed with DILI. HDS was determined as the causative agent in 28 out of those 32 patients. The MH cell test could correctly identify 29 out of those 32 DILI cases and showed false positive results in only 2 out of the 15 non-DILI patients. The MH cell test therefore reached a sensitivity and specificity of 90.6 and 86.7%, respectively, in patients with acute liver injury and HDS intake. <b><i>Conclusions:</i></b> Our data provide evidence that the MH cell test can be a useful tool to identify the role of HDS in causing DILI and therefore support causality assessment in patients consuming HDS.
DOI: 10.6084/m9.figshare.12674357
title: CNV calling in MUG goats

description: Copy number variation (CNV) mapping in a population of 1036 Murciano-Granadina goats
DOI: 10.6084/m9.figshare.12674372
title: Data to run the analyses in the paper "Tropical and Mediterranean biodiversity is disproportionately sensitive to land-use and climate change"

description: This dataset contains an archive of all the data needed to replicate the main analyses in the paper.
DOI: 10.6084/m9.figshare.12674381
title: Kaggle_NLP_Notebooks.zip

description: Manually annotated all notebooks
DOI: 10.6084/m9.figshare.12674324
title: BEH 3612 Supplementary data

description: Behaviours in the mirror and tonic immobility tests, per individual ID, sex and period at which birds were tested.
DOI: 10.6084/m9.figshare.12674381.v2
title: Kaggle_NLP_Notebooks.zip

description: Manually annotated all notebooks
DOI: 10.6084/m9.figshare.12674291
title: Semantics_based_source_code_ labels.xlsx

description: This is the dataset of semantic labels from all labelled notebooks.
DOI: 10.6084/m9.figshare.12674324.v1
title: BEH 3612 Supplementary data

description: Behaviours in the mirror and tonic immobility tests, per individual ID, sex and period at which birds were tested.
DOI: 10.6084/m9.figshare.12674231
title: It matters who you know, down below: Different mycorrhizal fungal communities differentially affect plant phenolic defences against herbivory

description: Frew A, Wilson BAL. 2020 It matters who you know, down below: Different mycorrhizal fungal communities differentially affect plant phenolic defences against herbivory<br><b>Data:</b>Plant biomass;plant chemistry;insect herbivore performance;arbuscular mycorrhizal fungal root colonisation.
DOI: 10.6084/m9.figshare.12674228
title: Basic characteristics of the included studies

description: This is a basic characteristics of the included studies
DOI: 10.6084/m9.figshare.12674219
title: Source Data for Vjestica et al. 2020

description: The single ZIP file contains Supplemental Sequences and Source Data for Vjestica et al. 2020<br>
DOI: 10.6084/m9.figshare.12674291.v1
title: Semantics_based_source_code_ labels.xlsx

description: This is the dataset of semantic labels from all labelled notebooks.
DOI: 10.6084/m9.figshare.12674219.v1
title: Source Data for Vjestica et al. 2020

description: The single ZIP file contains Supplemental Sequences and Source Data for Vjestica et al. 2020<br>
DOI: 10.6084/m9.figshare.12674231.v1
title: It matters who you know, down below: Different mycorrhizal fungal communities differentially affect plant phenolic defences against herbivory

description: Frew A, Wilson BAL. 2020 It matters who you know, down below: Different mycorrhizal fungal communities differentially affect plant phenolic defences against herbivory<br><b>Data:</b>Plant biomass;plant chemistry;insect herbivore performance;arbuscular mycorrhizal fungal root colonisation.
DOI: 10.6084/m9.figshare.12674189
title: Bracon brevicornis linked-read genome assembly PRJEB35412

description: Presented here is the <i>Bracon brevicornis</i> genome assembly (fasta file). Also available via the ENA (BioProject PRJEB35412), presented here as an additional file resource. Briefly, this is a 10X Genomics linked-read assembly, where <i>B. brevicornis</i> females of a fairly inbred lab strain were used in the DNA extraction. This DNA isolation was used in concert with DNA from a known specimen of an unrelated (plant) species where the other DNA was carrier DNA to ensure that the 10X Genomics reaction succeeded. More is explained in the forthcoming preprint (NB: to be added after it is preprinted).<br>
DOI: 10.6084/m9.figshare.12674228.v2
title: Basic characteristics of the included studies

description: This is a basic characteristics of the included studies
DOI: 10.6084/m9.figshare.12674228.v1
title: Basic Characteristics of the Included Studies.docx

description: This is a Table of Basic Characteristics of the Included Studies
DOI: 10.6084/m9.figshare.12674063
title: Supplementary Material for: Remote Ischemic Preconditioning Reduces the Risk of Contrast-Induced Nephropathy in Patients with Moderate Renal Impairment Undergoing Percutaneous Coronary Angiography: A Meta-Analysis

description: <b><i>Background/Aims:</i></b> This meta-analysis evaluated the effects of remote ischemic preconditioning (RIPC) on the risk of contrast-induced nephropathy (CIN) in patients undergoing percutaneous coronary intervention/coronary angiography (PCI/CA). <b><i>Methods:</i></b> PubMed, Embase, and the Cochrane Central Register of Controlled Trials databases were searched for randomized controlled trials (RCTs) that assessed the effect of RIPC on CIN in patients undergoing PCI/CA. The main outcomes of interest were the incidence of CIN 48–72 h after CA, the levels of serum creatinine, cystatin C, neutrophil gelatinase-associated lipocalin, and estimated glomerular filtration rate (eGFR), mortality, and requirement of hemodialysis and rehospitalization. The analysis was conducted using the random-effect model due to the expected heterogeneity among different studies. <b><i>Results:</i></b> In total, 16 trials covering 2,048 patients were identified. By assessing the methodological quality of the included studies through the Coch­rane risk of bias, we found that of the 16 RCTs, 3 had a low risk of bias, 6 a high, and 7 an unclear risk. The application of RIPC decreased the incidence of CIN (relative risk, RR, 0.50, 95% confidence interval, CI, 0.39–0.65; <i>p</i> &lt; 0.001). Subgroup analyses showed that RIPC decreased the incidence of CIN in patients with eGFR &lt;60 mL/min/1.73 m<sup>2</sup> (RR 0.53, 95% CI 0.38–0.75; <i>p</i> &lt; 0.001) but not in patients with eGRF ≥60 mL/min/1.73 m<sup>2</sup> (RR 0.82, 95% CI 0.35–1.94; <i>p</i> = 0.66) at baseline. Furthermore, the increase in serum creatinine was significantly lower in patients with RIPC compared to control patients (standardized mean difference –1.41, 95% CI –2.46 to –0.35; <i>p</i> = 0.009). <b><i>Conclusions:</i></b> Based on 16 RCTs, this meta-analysis shows that RIPC can reduce the risk of CIN in patients with moderate renal impairment undergoing PCI/CA. However, this needs to be confirmed by further high-quality evidence.