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  1. Woods Hole Open Access Server

    Title: Trial A test of the dissolution method for estimates of the 15N2 atom% of incubations

    Dataset 2019-10-02

    Contributors:
    Summary: The “dissolution” method to measure N2 fixation rates with 15N2 gas tracer involves the preparation of 15N2-enriched water that is then added to each incubation bottle. Investigators typically measure the 15N2 atom% of the 15N2-enriched inoculum by MIMS, and extrapolate the 15N2 atom% in the incubations based on the inoculum value. Here, we demonstrate that such extrapolation yields inaccurate estimates of the 15N2 atom% of incubations. The latter should be measured directly. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/778126

  2. Woods Hole Open Access Server

    Title: Test of integrity of dissolved 15N2 gas samples stored in Exetainer vials

    Dataset 2019-10-02

    Contributors:
    Summary: We monitored the 15N2 gas atom% values of prepared solutions stored in Exetainer vials (filled with no headspace) in order to verify that these values remained stable over a period of weeks to months of storage. The integrity of samples was preserved for at least 6 months. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/778047

  3. Woods Hole Open Access Server

    Title: Nutrient and nitrate isotope data from the southern Benguela upwelling system from February to August 2017

    Dataset 2020-05-20

    Contributors:
    Summary: Analysed Particulate Organic Matter data, Nutrient data and Nitrate isotope data from the 2017 Integrated Ecosystem Programme: Southern Benguela (IEP:SB) cruises conducted in February, May, and August 2017. The IEP:SB is a multi-disciplinary, multi-institutional platform to undertake relevant science in the Southern Benguela; also functioning as a platform for collaboration and learning. Nitrate+nitrite concentrations were measured on a Lachat QuickChem flow injection analysis platform in a configuration with a detection limit of 0.1 µM, while phosphate and nitrite concentrations were measured using standard benchtop techniques on a Thermo Scientific Genesis 30 Visible spectrophotometer in a configuration with a detection limit of 0.05 µM. The N and O isotope ratios of the N2O gas were analysed using a Delta V Advantage continuous flow isotope ratio mass spectrometer interfaced with an online N2O extraction and purification system. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/811839

  4. Woods Hole Open Access Server

    Title: Trial B test of the dissolution method for estimates of the 15N2 atom% of incubations

    Dataset 2019-10-02

    Contributors:
    Summary: The “dissolution” method to measure N2 fixation rates with 15N2 gas tracer involves the preparation of 15N2-enriched water that is then added to each incubation bottle. Investigators typically measure the 15N2 atom% of the 15N2-enriched inoculum by MIMS, and extrapolate the 15N2 atom% in the incubations based on the inoculum value. Here, we demonstrate that such extrapolation yields inaccurate estimates of the 15N2 atom% of incubations. The latter should be measured directly. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/778158

  5. Woods Hole Open Access Server

    Title: Analyses of nitrate reference solutions in 18O-labeled water with the denitrifier method (Biological Nitrogen Isotope Fractionation project)

    Dataset 2022-01-14

    Contributors:
    Summary: IAEA-NO3 and USGS-34 reference solutions were supplemented with 18O-labeled water and analyzed for N and O isotope ratios. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/865519

  6. Woods Hole Open Access Server

    Title: Volume effects on blanks originating from the bacterial concentrates, equilibration with atmospheric N2O, and NO3- contamination of the water into which the standards were diluted from 2017-2020 (Biological Nitrogen Isotope Fractionation project)

    Dataset 2022-01-14

    Contributors:
    Summary: Volume-dependent N2O blanks originating from the bacterial concentrates, equilibration with atmospheric N2O, and NO3- contamination of the water into which the standards were diluted. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/865089

  7. Woods Hole Open Access Server

    Title: Comparison of Membrane Inlet Mass Spectrometry (MIMS) to Isotope Ratio Mass Spectrometer (IRMS)

    Dataset 2019-10-02

    Contributors:
    Summary: In order to ensure that 15N2 atom% effectuated by Membrane Inlet Mass Spectrometry, we tested whether the mass-specific signal ratios returned by MIMS are equivalent with parallel measurements on a Isotope Ratio Mass Spectrometer, on the basis that the latter returns accurate ratios (see 778000 cal_iso). MIMS and IRMS returned identical values for parallel samples. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/778065

  8. Woods Hole Open Access Server

    Title: Analysis of dissolved 15N2 gas standards by Membrane Inlet Mass Spectrometry

    Dataset 2019-10-02

    Contributors:
    Summary: In order to verify that measurements of the 15N2 atom% of dissolved N2 gas samples effectuated by Membrane Inlet Mass Spectrometry are accurate, we developed a specific protocol to prepare dissolved 15N2 gas standards. We detail the protocol herein, and report representative MIMS measurements of the prepared standards. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/778021

  9. Woods Hole Open Access Server

    Title: Effects of sample volume on N2O recovery and isotopic analysis (Biological Nitrogen Isotope Fractionation project)

    Dataset 2022-01-14

    Contributors:
    Summary: Incomplete N2O analyte recovery during sparging of high-volume samples and associated N and O isotopic ratio offsets. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/865053

  10. Woods Hole Open Access Server

    Title: ẟ15N (ẟ18O) scale contraction was calculated as the percent deviation of the difference between measured ẟ15N (ẟ18O) values of IAEA-NO3 and USGS-34 from the true difference (Biological Nitrogen Isotope Fractionation project)

    Dataset 2022-01-14

    Contributors:
    Summary: ẟ15N (ẟ18O) scale contraction was calculated as the percent deviation of the difference between measured ẟ15N (ẟ18O) values of IAEA-NO3 and USGS-34 from the true difference. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/865043

  11. Woods Hole Open Access Server

    Title: Nitrate N and O isotope ratios from CTD niskin depth profiles collected along section HLY1502-GN01 in the Western Arctic Ocean from August to October 2015

    Dataset 2020-07-27

    Contributors:
    Summary: High precision measurements of Nitrogen (15N/14N) and Oxygen (18O/16O) isotope ratios in depth profiles along the GEOTRACES transect to the western Arctic Ocean (HLY1502-GN01) were made in order to trace nitrogen cycling in different parts of the basin and within different water masses. Nitrate isotope ratio analyses were performed by Richard Dabundo in the Granger Laboratory at the University of Connecticut. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/733109

  12. Woods Hole Open Access Server

    Title: Test of potential mass to charge 30 interferences from O2

    Dataset 2019-10-02

    Contributors:
    Summary: Molecular oxygen (O2) has been documented to ionize partially to NO+ in mass spectrometer sources, generating a signal that overlaps with that of 15N2 (mass-to-charge of 30). Here, we tested whether O2 needs to be specifically removed from the sample streams of the Membrane Inlet Mass Spectrometer and the Isotope Ratio Mass Spectrometer in order to properly quantitate 15N2 atom% at pertinent concentrations. Sample streams with and without O2 yielded similar signals, suggesting that O2 does not interfere with the 15N2 atom% measurements in the experimental range with the given instruments. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/778083

  13. Woods Hole Open Access Server

    Title: Simulation of the volume-dependent changes in ẟ15N and ẟ18O for IAEA-NO3 and USGS-34 reference materials (Biological Nitrogen Isotope Fractionation project)

    Dataset 2022-01-14

    Contributors:
    Summary: Simulation of the volume-dependent changes in ẟ15N and ẟ18O for IAEA-NO3 and USGS-34 reference materials. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/865685

  14. Woods Hole Open Access Server

    Title: Simulation of δ15N and δ18O scale contraction, given the observation of the fraction of O atom exchange with water and blanks (Biological Nitrogen Isotope Fractionation project)

    Dataset 2022-01-14

    Contributors:
    Summary: Simulation of δ15N and δ18O scale contraction, given the observation of the fraction of O atom exchange with water and blanks. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/865676

  15. Woods Hole Open Access Server

    Title: O exchange with water during denitrification with the denitrifier method (Biological Nitrogen Isotope Fractionation project)

    Dataset 2022-01-14

    Contributors:
    Summary: Effects of sample volume and salinity on O atom exchange with water during denitrification with the denitrifier method. The percentages of O atom exchange were derived from the regression slopes of ẟ18ON2O vs. ẟ18OH2O. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/865666

  16. Woods Hole Open Access Server

    Title: Volume-dependent offsets in NO3- N and O isotope ratios of reference materials (Biological Nitrogen Isotope Fractionation project)

    Dataset 2022-01-14

    Contributors:
    Summary: NO3- reference materials (IAEA-NO3 and USGS-34) in seawater and freshwater were used to demonstrate volume-dependent offsets of NO3- N and O isotope ratio analyses with the denitrifier method. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/865031

  17. Woods Hole Open Access Server

    Title: Calibration of the Isotope Ratio Mass Spectrometer vs. aliquots of 15N2 gas diluted in air then helium

    Dataset 2019-10-02

    Contributors:
    Summary: In order to verify that measurements of the 15N2 atom% of dissolved N2 gas samples effectuated by Membrane Inlet Mass Spectrometry are accurate, we compared these to corresponding measurements of parallel samples on a Delta V Isotope Ratio Mass Spectrometer (IRMS). To this end, we first ensured that the IRMS returns accurate 15N2 atom% values, by measuring the 15N2 atom% of a serial dilutions of a 15N2 gas stock in air and helium. This calibration is documented herein, showing that IRMS measurements in the experimental range were accurate, as expected For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/778000

  18. Zenodo

    Title: nbgrader v0.5.5

    Software 2019

    Contributors:
    Subjects:
    • jupyter
    • nbgrader
    • education
    • grading
    Summary:

    nbgrader version 0.5.5 is a release for the Journal of Open Source education,
    with the following PRs merged:

    • PR #1057: Ensure consistency in capitalizing Jupyter Notebook
    • PR #1049: Update test builds on Travis
    • PR #1047: JOSE paper bib updates
    • PR #1045: Dev requirements and spelling tests
    • PR #1016: Fix anaconda link
    • PR #973: Create a paper on nbgrader

    Thanks to the following users who submitted PRs or reported issues that were fixed for the 0.5.5 release:

    • jedbrown
    • jhamrick
    • swarnava
    • willingc

  19. Zenodo

    Title: edgeR version 3.8

    Software 2014

    Contributors:
    Summary:

    edgeR is an R package distributed as part of the Bioconductor project (http://www.bioconductor.org). The Galaxy tool that implements this workflow is available from http://toolshed.g2.bx.psu.edu/view/shians/shrnaseq.

  20. Zenodo

    Title: GIANT: Galaxy-based Interactive tools for ANalysis of Transcriptomic data

    Software 2018

    Contributors:
    Summary:

    GIANT is a User-friendly tools suite for micro-arrays analyses and for exploring RNA-seq & Micro-Arrays differential results