cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7284/130034
title: Timeserver data collected during research cruise OC1807B using a Microsemi SyncServer S350 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/129861
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise OC1808A using a Hawaii UHDAS instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7374779
title: MOESM3 of Phenotypic and genetic variation in the response of chickens to Eimeria tenella induced coccidiosis

description: Additional file 3: Table S2. Univariate linear model analyses performed in ASReml 4.0 were used to predict the means (PM) of the fixed effects on each of the measured traits, with standard errors (Âąâ SE) and significance (P value).
DOI: 10.6084/m9.figshare.7374779.v1
title: MOESM3 of Phenotypic and genetic variation in the response of chickens to Eimeria tenella induced coccidiosis

description: Additional file 3: Table S2. Univariate linear model analyses performed in ASReml 4.0 were used to predict the means (PM) of the fixed effects on each of the measured traits, with standard errors (Âąâ SE) and significance (P value).
DOI: 10.7284/129864
title: Anemometer data collected during research cruise OC1808A using a Gill WindObserver II instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/129860
title: Fluorometer data collected during research cruise OC1808A using a WET Labs WETStar instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/129865
title: GNSS (Global Navigation Satellite System) data collected during research cruise OC1808A using a Furuno GP-90 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/129870
title: GNSS (Global Navigation Satellite System) data collected during research cruise OC1808A using a Ashtech ADU5 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/129858
title: Gyrocompass data collected during research cruise OC1808A using a Sperry MK-37 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/129859
title: PTU (Pressure, Temperature, Humidity) data collected during research cruise OC1808A using a Vaisala PTU300 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7374155
title: CRISPR-NHEJ data files

description: These files contain:3 replicates of processed data for CRISPR NHEJ profiling.1 CRPISPR NHEJ profiling with microhomology design1 table for machine learning training
DOI: 10.7284/129862
title: Radiometer data collected during research cruise OC1808A using a RMR Co. PRP instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7374155.v1
title: CRISPR-NHEJ replicates

description: These are 3 replicates of processed data for CRISPR NHEJ profiling.
DOI: 10.6084/m9.figshare.7374155.v2
title: CRISPR-NHEJ data files

description: These files contain:3 replicates of processed data for CRISPR NHEJ profiling.1 CRPISPR NHEJ profiling with microhomology design1 table for machine learning training
DOI: 10.7284/129863
title: Water Temperature data collected during research cruise OC1808A using a Sea-Bird SBE-38 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7374155.v3
title: CRISPR-NHEJ data files

description: These files contain:3 replicates of processed data for CRISPR NHEJ profiling.1 CRPISPR NHEJ profiling with microhomology design1 table for machine learning training
DOI: 10.7284/129868
title: Water Temperature data collected during research cruise OC1808A using a Sea-Bird SBE-48 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7374155.v4
title: CRISPR-NHEJ data files

description: These files contain:3 replicates of processed data for CRISPR NHEJ profiling.1 CRPISPR NHEJ profiling with microhomology design1 table for machine learning training
DOI: 10.7284/129867
title: Timeserver data collected during research cruise OC1808A using a Microsemi SyncServer S350 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7374155.v5
title: CRISPR-NHEJ data files

description: These files contain:3 replicates of processed data for CRISPR NHEJ profiling.1 CRPISPR NHEJ profiling with microhomology design1 table for machine learning training
DOI: 10.7284/130041
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise OC1808B using a Hawaii UHDAS instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7374071
title: Immunofluorescence_Y27632 treated

description: SOX9 (green), actin (red), nucleus (blue) confocal micrographs of control and cLIUS (us) samples treated with Y27632
DOI: 10.6084/m9.figshare.7374071.v1
title: Immunofluorescence_Y27632 treated

description: SOX9 (green), actin (red), nucleus (blue) confocal micrographs of control and cLIUS (us) samples treated with Y27632
DOI: 10.7284/130044
title: Anemometer data collected during research cruise OC1808B using a Gill WindObserver II instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7373906
title: GFB1 Science Response to eLetters Figure&Rscript

description: Estimated BPR curve (with 95% confidence interval bands), using an ordinary least squares (OLS) model, based on the three grassland biomes (i.e. Montane Grasslands and Shrublands, Flooded Grasslands and Savannas, and Temperate Grasslands, Savannas and Shrublands). We converted species richness (S) to relative species richness (S_hat): S_hat = S *100 / 271.<br>R script for generating this graph is attached.
DOI: 10.6084/m9.figshare.7373870
title: Placenta 10X raw counts samples

description: Placenta samples (6) from the dataset used in Vento-Tormo et al. 2018. Used for analysis in the EmptyDrops manuscript.
DOI: 10.6084/m9.figshare.7373876
title: Analysis_high-speed-footage

description: Analysis of the high-speed video footag. CSV file counting attack success of <i>Chaoborus </i>larva in the high-speed footage.<br>1. column 'file': name of the corresponding avi-file <br>2. column 'Treatment': either 'Ctrl' or 'Ind'; referring to the morphotype of the used daphniid. That was undefended (Ctrl) or defended (Ind).<br>3. column 'attack successful': either 'Yes' or 'No'; outcome of the <i>Chaoborus </i>larva attack in the corresponding footage. Prey ingestion equals 'Yes', prey escape equals 'No'.<br>4. column 'attack succesful 1/0': either '1' or '0'; same information as 3. column, '1' equals 'Yes' in the 3. column, '0' equals 'No' in 3. column.<br>5. column 'Prey morph': either 'Undefended' or 'Defended'; Morphotype of the daphniid used in the corresponding footage.
DOI: 10.6084/m9.figshare.7373903
title: Analysis_predation-trials

description: Analysis of the predation trial videos. CSV file including number of attacks, number of prey evasions, contact, ingestions and escapes.<br>1. column 'file': name of the corresponding avi-file<br>2. column 'prey morph': either 'Undefended' or 'Defended'; Morphotype of the daphniids used in the corresponding footage.<br>3. column 'replicate number': consecutive number referring to the experiment's replicate of the corresponding avi file.<br>4. column 'sum of strike': total number of strikes of the used <i>Chaoborus </i>larva on the prey daphniids in the corresponding replicate/footage.<br>5. column 'sum of evasion': total number of prey evasions after a predator strike in the corresponding replicate/footage.<br>6. column 'sum of contact': total number of prey contacts as a result of predator strikes in the corresponding replicate/footage.<br>7. column 'sum of ingestion': total number of prey ingestions after prey contact in the corresponding replicate/footage.<br>8. column 'sum of escapes': total number of prey espaces after prey contact in the corresponding replicate/footage.<br>9. column 'evasion [%]': percentage of prey evasions per predator strikes in the corresponding replicate/footage.<br>10. column 'contact [%]': percentage of prey contacts per predator strikes in the corresponding replicate/footage.<br>11. column 'ingestion [%]': percentage of prey ingestions per prey contacts in the corresponding replicate/footage.<br>12. column 'escape [%]': percentage of prey escapes per prey contacs in the corresponding replicate/footage.
DOI: 10.7284/130040
title: Fluorometer data collected during research cruise OC1808B using a WET Labs WETStar instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7373870.v1
title: Placenta 10X raw counts samples

description: Placenta samples (6) from the dataset used in Vento-Tormo et al. 2018. Used for analysis in the EmptyDrops manuscript.
DOI: 10.6084/m9.figshare.7373903.v1
title: Analysis_predation-trials

description: Analysis of the predation trial videos. CSV file including number of attacks, number of prey evasions, contact, ingestions and escapes.<br>1. column 'file': name of the corresponding avi-file<br>2. column 'prey morph': either 'Undefended' or 'Defended'; Morphotype of the daphniids used in the corresponding footage.<br>3. column 'replicate number': consecutive number referring to the experiment's replicate of the corresponding avi file.<br>4. column 'sum of strike': total number of strikes of the used <i>Chaoborus </i>larva on the prey daphniids in the corresponding replicate/footage.<br>5. column 'sum of evasion': total number of prey evasions after a predator strike in the corresponding replicate/footage.<br>6. column 'sum of contact': total number of prey contacts as a result of predator strikes in the corresponding replicate/footage.<br>7. column 'sum of ingestion': total number of prey ingestions after prey contact in the corresponding replicate/footage.<br>8. column 'sum of escapes': total number of prey espaces after prey contact in the corresponding replicate/footage.<br>9. column 'evasion [%]': percentage of prey evasions per predator strikes in the corresponding replicate/footage.<br>10. column 'contact [%]': percentage of prey contacts per predator strikes in the corresponding replicate/footage.<br>11. column 'ingestion [%]': percentage of prey ingestions per prey contacts in the corresponding replicate/footage.<br>12. column 'escape [%]': percentage of prey escapes per prey contacs in the corresponding replicate/footage.
DOI: 10.7284/130045
title: GNSS (Global Navigation Satellite System) data collected during research cruise OC1808B using a Furuno GP-90 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130051
title: GNSS (Global Navigation Satellite System) data collected during research cruise OC1808B using a Ashtech ADU5 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130038
title: Gyrocompass data collected during research cruise OC1808B using a Sperry MK-37 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130039
title: PTU (Pressure, Temperature, Humidity) data collected during research cruise OC1808B using a Vaisala PTU300 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130043
title: Water Temperature data collected during research cruise OC1808B using a Sea-Bird SBE-38 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7371191
title: Diverse genotypes of the amphibian killing fungus produce distinct phenotypes through plastic responses to temperature

description: Dataset consists of two raw data files, four generated files during analyses, a phylogenetic tree file and two R files (one raw code, one markdown):<br>Raw data files<br>1) Size data. Zoospore and zoosporangium size measurements titled “BdSizeMeasurements.csv”. This file consists of all size measurements taken for each Bd genotype. The area of the measurement was used in linear mixed-effects models to analyze the effect of temperature, genotype and their interaction on size. <br>2) Growth data. Plate read measurements for growth rate titled "GR_data.csv". This file consists of all OD readings for every well for every day that readings were taken. We used R code to correct baseline zoospore OD, remove wells with potential contamination, fit logistic growth models, and then extracted parameter estimates to use in linear mixed-effects models.<br>Four files generated from the raw data files in the R code to test for phylogenetic signal. I chose to make files in excel as opposed to just writing code to create R data frames.<br>1) Linear mixed-effects model estimates titled “parameters_size_gr.csv”. These are the mean model estimates from the linear mixed-effects models conducted on size and growth data. <br>2) Relative distance plasticity index (RDPI) for each trait titled “rdpi_size_gr.csv”. We calculated RDPI (Valladares et al., 2006) for each trait using the function rdpi in the package ‘Plasticity’ (Ameztegui, 2017. <br>3 and 4) A second way to visualize the mean model estimates from the linear mixed effects models. These files were created to generate figures 5 and 6 in the publication.<br>Phylogenetic tree is titled “carly_strains.tre” and is a tree constructed using the neighbor-joining algorithm in PAUP*4.0 based on concatenated multilocus genotypes for 36 loci from multiple chromosomal regions (Schloegel et al., 2012, Jenkinson et al., 2016).<br>R file is titled “PhenoProject_final_submit.Rmd” and the knitted .Rmd file (with all of the code and output run) is titled “PhenoProject_final_submit.html”<br>
DOI: 10.6084/m9.figshare.7371197
title: Lu et al., 2019, GRL

description: Dataset used to plot the figures in the manuscript of Lu et al. (2018) submitted to GRL.
DOI: 10.6084/m9.figshare.7372898
title: Simultaneous extracellular electrophysiology data

description: Supporting data for “An orderly single-trial organization of population dynamics in premotor cortex predicts behavioral variability”.<br>
DOI: 10.7284/130049
title: Water Temperature data collected during research cruise OC1808B using a Sea-Bird SBE-48 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7372898.v2
title: Simultaneous extracellular electrophysiology data

description: Supporting data for “An orderly single-trial organization of population dynamics in premotor cortex predicts behavioral variability”.<br>
DOI: 10.7284/130048
title: Timeserver data collected during research cruise OC1808B using a Microsemi SyncServer S350 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7371197.v1
title: data.rar

description: Dataset used to plot the figures in the manuscript of Lu et al. (2018) submitted to GRL.
DOI: 10.6084/m9.figshare.7371179
title: Haemochromatosis in UK Biobank - Pilling et al. 2019 BMJ

description: Supplementary Tables for UK Biobank study of Haemochromatosis published in the BMJ by Pilling et al. 2019<br>
DOI: 10.7284/130055
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise OC1808C using a Hawaii UHDAS instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130058
title: Anemometer data collected during research cruise OC1808C using a Gill WindObserver II instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130054
title: Fluorometer data collected during research cruise OC1808C using a WET Labs WETStar instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130059
title: GNSS (Global Navigation Satellite System) data collected during research cruise OC1808C using a Furuno GP-90 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130065
title: GNSS (Global Navigation Satellite System) data collected during research cruise OC1808C using a Ashtech ADU5 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130052
title: Gyrocompass data collected during research cruise OC1808C using a Sperry MK-37 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130053
title: PTU (Pressure, Temperature, Humidity) data collected during research cruise OC1808C using a Vaisala PTU300 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130056
title: Radiometer data collected during research cruise OC1808C using a RMR Co. PRP instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130057
title: Water Temperature data collected during research cruise OC1808C using a Sea-Bird SBE-38 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130063
title: Water Temperature data collected during research cruise OC1808C using a Sea-Bird SBE-48 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130062
title: Timeserver data collected during research cruise OC1808C using a Microsemi SyncServer S350 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130069
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise OC1808X using a Hawaii UHDAS instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7370885
title: Supplementary Material for: Cognitive Status and Functional Dexterity as Outcome Predictors Following Urinary Diversion: A Combined Retrospective and Prospective Observational Study

description: <b><i>Purpose:</i></b> The study aimed to evaluate the impact of the validated functional dexterity test and the Mini-Mental Status test on subjective functional outcomes, medical care situation, and health-related quality of life (HRQoL) after urinary diversion (UD). <b><i>Patients and Methods:</i></b> A total of 106 patients (<i>n</i> = 26 ileal conduits, <i>n</i> = 29 neobladders, and <i>n</i> = 51 ileocecal pouches) were included in this combined retrospective (<i>n</i> = 77) and prospective (<i>n</i> = 29) observational study. All patients performed the 2 tests mentioned above and filled out self-designed questionnaires with diversion and HRQoL items. In the prospective cohort, the tests were performed preoperatively and the questionnaires were filled out preoperatively as well as 3 and 6 months after surgery. <b><i>Results:</i></b> Reduced dexterity and cognitive skills were significantly associated with increased patient age and subjective constraints in stoma care of ileal conduits, self-catheterization in ileocecal pouches, and continence in neobladders. Overall HRQoL, however, was not affected by dexterity or cognitive measures. <b><i>Conclusions:</i></b> Assessing the cognitive status and functional dexterity of patients undergoing UD might provide a useful objective clinical tool to aid in decision-making regarding the type of UD and postoperative medical care situation. Further prospective data are needed to confirm these findings and further simplify the methods used here.
DOI: 10.6084/m9.figshare.7370852
title: Supplementary Material for: Genome-Scale Single Nucleotide Resolution Analysis of DNA Methylation in Human Autosomal Dominant Polycystic Kidney Disease

description: <b><i>Background:</i></b> Autosomal dominant polycystic kidney disease (ADPKD) is characterized by the formation of fluid-filled cysts in the kidney and end stage renal disease by the fourth or fifth decade of life. Mutations in the <i>PKD1</i> gene account for 85% of all cases of ADPKD. No curative therapy exists for patients affected by this disease and an underexplored avenue for the treatment of ADPKD is the targeting of epigenetic changes that occur during cystogenesis. Limited data exists on alterations in DNA methylation that are associated with ADPKD. Given the similarities between cyst growth and neoplasia, and the fact that 2 DNA methylation inhibitors are already Food and Drug Administration-approved for the treatment of myelodysplastic syndrome, we hypothesized that global DNA methylation patterns in ADPKD would parallel that observed in neoplasia, and which may provide an opportunity to treat ADPKD with epigenetic inhibitors. To address this hypothesis, we undertook a global DNA methylation analysis of human ADPKD kidney. <b><i>Methods:</i></b> We generated single nucleotide resolution methylomes of cortical kidney tissue from individuals with ADPKD, and from non-ADPKD kidney tissue, using reduced representation bisulfite sequencing. Using quantitative reverse transcription polymerase chain reaction, we investigated expression of the <i>PKD1</i> gene in both ADPKD and non-ADPKD kidney. <b><i>Results:</i></b> We have shown that ADPKD-derived genomic DNA exhibits global hypomethylation when compared with non-ADPKD kidney, a pattern commonly observed in DNA methylation studies of tumor-derived tissue. We have also identified 13 discrete regions that are significantly differentially methylated in ADPKD compared to non-ADPKD, and 8 of these are gene specific. The <i>PKD1</i> gene shows an increase in methylation at the 3′ end of the gene body, but in contrast to previously published data, this is not associated with a decrease in <i>PKD1</i> mRNA expression. <b><i>Conclusion:</i></b> This genome-scale single nucleotide resolution analysis of DNA methylation in human polycystic kidneys suggests that DNA methylation differences at specific loci are associated with ADPKD. Further exploration into the significance of these preliminary results may shed light on the disease process, and potentially reveal new therapeutic possibilities.