cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10581300
title: Reduction of NQO1 wildtype by NADD

description: Raw data published in: Anoz-Carbonell E, Timson DJ, Pey AL, Medina M. The Catalytic Cycle of the Antioxidant and Cancer-Associated Human NQO1 Enzyme: Hydride Transfer, Conformational Dynamics and Functional Cooperativity. Antioxidants (Basel). 2020 Aug 20;9(9):772. doi: 10.3390/antiox9090772. PMID: 32825392; PMCID: PMC7554937.

Data measured using a stopped-flow spectrophotometer from Applied Photophysics (SX.18MV, Applied Photophysics Ltd., Leatherhead, UK) interfaced with a photodiode array detector and under anaerobic conditions, following previously established protocols. Multiple wavelength absorption data in the flavin absorption region (400-900 nm) were collected and processed using the ProData-SX software (Applied Photophysics Ltd.). Time-dependent spectral deconvolution was performed by global analysis and numerical integration methods using Pro-Kineticist (Applied Photophysics Ltd.). Collected data were fitted to either single- or multi-step (A→B→n….→Z) models allowing for estimation of the corresponding observed conversion rate constants at each NADH concentration, as well of the spectra of intermediate and final species.

NQO1ox (7.5 μM) was mixed with NADD at concentrations ranging from 1:1 to 1:14 NQO1ox:NADH ratio. Reactions were studied in 20 mM HEPES-KOH, pH 7.4 with glucose/glucose oxidase (310 mM/10 units/mL), at 25 C.

Spectral evolution of NQO1 reductive half-reaction with NADD at different concentrations. Files are numbered from 1 to 7 representing the following NADD concentrations: 7.5, 10, 15, 20, 30, 50 and 100 uM of NADD.
DOI: 10.5281/zenodo.10527309
title: Experiments on hydraulic jumps over uneven bed for turbulent flow modelling validation in river flow and hydraulic structures

description: Experimental dataset of laboratory experiments on hydraulic jumps over uneven beds for turbulent flow modelling conducted at the University of Cordoba.
DOI: 10.5281/zenodo.10527310
title: Experiments on hydraulic jumps over uneven bed for turbulent flow modelling validation in river flow and hydraulic structures
DOI: 10.5281/zenodo.10581318
title: Experiments on hydraulic jumps over uneven bed for turbulent flow modelling validation in river flow and hydraulic structures

description: Experimental dataset of laboratory experiments on hydraulic jumps over uneven beds for turbulent flow modelling conducted at the University of Cordoba.
DOI: 10.5281/zenodo.10581376
title: Reactivity of ClDaf and Pyr with different metalic salts

description: Evaluation of the reactivity of ClDaf and Pyridomycin when mixed with 10 equivalents of different metalic salts. 

Samples were analyzed by analytical UPLC. 

Analytical (non-high resolution) spectrometry analysis (UHPLC-MS) were performed on an Ultimate 3000 UHPLC system, coupled with a LCQ Fleet Ion Trap Mass Spectrometer (Thermo Scientific). Chromatographic separation was achieved using an Acquity UPLC Peptide BEH C18 Column (300Å, 1.7 µm, 2.1 mm X 100 mm). Mobile phase system was composed of solvent A (H2O, 0.1% formic acid) and B (acetonitrile, 0.1% formic acid), typically run through a linear gradient from 0% to 100% of solvent B in 10 min. Elution of compounds was monitored by UV absorbance at 215 nm and 254 nm, and by mass spectrometry by electrospray ionization.

Data published in: Caradec T, Anoz-Carbonell E, Petrov R, Billamboz M, Antraygues K, Cantrelle FX, Boll E, Beury D, Hot D, Drobecq H, Trivelli X, Hartkoorn RC. A Novel Natural Siderophore Antibiotic Conjugate Reveals a Chemical Approach to Macromolecule Coupling. ACS Cent Sci. 2023 Nov 10;9(11):2138-2149. doi: 10.1021/acscentsci.3c00965. PMID: 38033789; PMCID: PMC10683483.
DOI: 10.5281/zenodo.10581377
title: Reactivity of ClDaf and Pyr with different metalic salts

description: Evaluation of the reactivity of ClDaf and Pyridomycin when mixed with 10 equivalents of different metalic salts. 

Samples were analyzed by analytical UPLC. 

Analytical (non-high resolution) spectrometry analysis (UHPLC-MS) were performed on an Ultimate 3000 UHPLC system, coupled with a LCQ Fleet Ion Trap Mass Spectrometer (Thermo Scientific). Chromatographic separation was achieved using an Acquity UPLC Peptide BEH C18 Column (300Å, 1.7 µm, 2.1 mm X 100 mm). Mobile phase system was composed of solvent A (H2O, 0.1% formic acid) and B (acetonitrile, 0.1% formic acid), typically run through a linear gradient from 0% to 100% of solvent B in 10 min. Elution of compounds was monitored by UV absorbance at 215 nm and 254 nm, and by mass spectrometry by electrospray ionization.

Data published in: Caradec T, Anoz-Carbonell E, Petrov R, Billamboz M, Antraygues K, Cantrelle FX, Boll E, Beury D, Hot D, Drobecq H, Trivelli X, Hartkoorn RC. A Novel Natural Siderophore Antibiotic Conjugate Reveals a Chemical Approach to Macromolecule Coupling. ACS Cent Sci. 2023 Nov 10;9(11):2138-2149. doi: 10.1021/acscentsci.3c00965. PMID: 38033789; PMCID: PMC10683483.
DOI: 10.5281/zenodo.10581396
title: Analysis of metabolites produced by D.fulvum

description: UPLC analysis of the metabolites produced by the soil bacterium D. fulvum when cultured in GYM media at different pH.

Samples were analyzed by analytical UPLC. Analytical (non-high resolution) spectrometry analysis (UHPLC-MS) were performed on an Ultimate 3000 UHPLC system, coupled with a LCQ Fleet Ion Trap Mass Spectrometer (Thermo Scientific). Chromatographic separation was achieved using an Acquity UPLC Peptide BEH C18 Column (300Å, 1.7 µm, 2.1 mm X 100 mm). Mobile phase system was composed of solvent A (H2O, 0.1% formic acid) and B (acetonitrile, 0.1% formic acid), typically run through a linear gradient from 0% to 100% of solvent B in 10 min. Elution of compounds was monitored by UV absorbance at 215 nm and 254 nm, and by mass spectrometry by electrospray ionization.
DOI: 10.5281/zenodo.10581397
title: Analysis of metabolites produced by D.fulvum

description: UPLC analysis of the metabolites produced by the soil bacterium D. fulvum when cultured in GYM media at different pH.

Samples were analyzed by analytical UPLC. Analytical (non-high resolution) spectrometry analysis (UHPLC-MS) were performed on an Ultimate 3000 UHPLC system, coupled with a LCQ Fleet Ion Trap Mass Spectrometer (Thermo Scientific). Chromatographic separation was achieved using an Acquity UPLC Peptide BEH C18 Column (300Å, 1.7 µm, 2.1 mm X 100 mm). Mobile phase system was composed of solvent A (H2O, 0.1% formic acid) and B (acetonitrile, 0.1% formic acid), typically run through a linear gradient from 0% to 100% of solvent B in 10 min. Elution of compounds was monitored by UV absorbance at 215 nm and 254 nm, and by mass spectrometry by electrospray ionization.
DOI: 10.5281/zenodo.10581322
title: PSTIV3 Historical Occupational Coding system

description: This contains the PSTIV3 coding scheme for historical occupations.The files are described in the Readme file.
DOI: 10.5287/ora-exv8qxx5m
title: Data from: Single-protein optical holography

description: This repository contains the data and code necessary to reproduce the results presented in the paper "Single-protein optical holography" by JC Thiele, E Pfitzner, and P Kukura.
A preprint is available on bioRxiv: https://doi.org/10.1101/2023.08.14.552817

There are two folders:
- Code: The Python code to analyse the data and generate figures. The following files are included:
 - fig1b_simulate_complex_image.py: Generate the illustration found in Figure 1b of the article.
 - fig2_plot_panel.py: Generates the panel plot in Figure 2: camera images and intensity, amplitude, and phase time traces from detected particles in the 40 nm AuNP sample.
 - fig5_plot_panel.py: Generates the panel plot in Figure 5: contrast distributions for AuNPs in holographic and darkfield measurements, calculation of the specific excess polarisability of proteins.
 - analyse_AuNP_phaseramp.py: Analysis script to generate the "particle_fits_*.h5" used in Figure 2 and 5. Detection and fitting of immobilised particles for darkfield and phase-modulated holographic measurements.
 - requirements.txt: list of Python dependencies
 - Jupyter notebooks to analyse protein landing measurements.
- Data: The raw and analysed data stored as hdf5 files. The following data is included:
 - 20 repeats of phase-shifting measurements of immobilised gold nanoparticles (20 nm, 40 nm, 60 nm). The files "darkfieldX.h5" contains the darkfield measurement from all for cameras. The file "phaseX.h5" contains the reference and interferometric measurement from the corresponding field of view while the phase delay in the sample path was modulated.
 - In the folders of the nanoparticle measurement, "particle_fits_*.h5" are included containing the fit results (position, amplitude, phase, fit error) for the darkfield measurement (all cameras independently) and holographic measurements (for different focus positions and phase delays).
 - In the folders of "DynDPRD landing events" the movies and analysed landing events can be found. The subfolder Movies, contains four protein landing measurements (termed "2ul_MS1000_xxx") from two days and the corresponding buffer, darkfield, and phase-shifting measurements. Note that all .h5 files contain prealigned and 2x2 binned data for all four phase shifted cameras. The subfolder Landning events contains the detected and fitted landing events used in Figure 3 and 4.
DOI: 10.48443/nxvq-ga39
title: Root biomass and chemistry, periodic (DP1.10067.001)
title: RELEASE-2024

description: This data product contains the quality-controlled, native sampling resolution data from NEON's belowground biomass protocol. These data enable estimation of the amount of belowground plant biomass &lt;= 10 mm diameter within the area surrounding the NEON eddy covariance tower. At many sites this will also be the dominant vegetation type(s). Samples are collected once every five years. Whenever possible, NEON uses a 3-inch outside diameter (6.65 cm inside diameter) soil corer for belowground biomass sampling, with samples cored to 30 cm depth in order to be consistent with the sampling depth used for soil biogeochemistry and microbe sampling. All roots are sorted into three size category bins: &lt;1 mm, 1-2 mm, and 2-10 mm. After sorting, root material is dried, weighed, and analyzed, then any excess root material is archived in the NEON Biorepository and available upon request. For additional details, see the user guide, protocols, and science design listed in the Documentation section below. Products resulting from this sampling include root biomass by size class as well as root chemistry and stable isotope ratios. A summary table of analytical lab precision and accuracy is included in the expanded package.

Latency:
The expected time from data and/or sample collection in the field to data publication is as follows, for each of the data tables (in days) in the downloaded data package. See the Data Product User Guide for more information.

bbc_chemistryPooling: 90

bbc_dilution: 90

bbc_percore: 28

bbc_rootmass: 90

bbc_rootChemistry: 270

bgc\_CNiso\_externalSummary: 30
description: Each site is sampled every five years. At each terrestrial NEON site, roots are sampled from base plots (20-30) within the tower airshed (Tower plots). In each Tower plot, one or two clip cells (depending on plot size) are randomly chosen out of the pre-determined clip cell locations for root coring. The same clip cells are also used for annual aboveground Herbaceous Biomass sampling. In 20m x 20m Tower plots, two soil cores are sampled from one clip cell per bout. In 40m x 40m Tower plots soil core sampling occurs in two (out of four) randomly assigned 20m x 20m subplots, and two soil cores are sampled from one clip cell per subplot per bout. A root core is taken to 30 cm maximum depth from both the northern and southern end of the clip cell. Biomass per size category is pooled by clip strip prior to chemistry analyses, and only live or unsorted biomass is analyzed. Carbon and nitrogen concentrations and stable isotopes are measured, but other analyses are possible by requesting access to remaining root material from the NEON Biorepository. Instrumentation:
DOI: 10.48443/677j-7v15
title: Salt-based stream discharge (DP1.20193.001)
title: RELEASE-2024

description: This data product contains the quality-controlled, native sampling resolution data for NEON's Salt-based Discharge data product. The data for this data product is collected as part of the wadeable stream reaeration sampling protocol. Salt concentration data from both constant rate, NaCl or NaBr, and slug, NaCl, injections at wadeable stream sites are published as part of this data product. Data users should refer to the user guide for reaeration and salt-based discharge (see `NEON_ReaerSaltBasedQ_userGuide`) for suggestions on how to calculate discharge values from the published data packages. For additional details, see the user guide, protocols, and science design listed in the Documentation section in this data product's details webpage.

Latency:
The expected time from data and/or sample collection in the field to data publication is as follows, for each of the data tables (in days) in the downloaded data package. See the Data Product User Guide for more information.

sbd_backgroundFieldCondData: 30

sbd_backgroundFieldSaltData: 30

sbd_conductivityFieldData: 30

sbd_externalLabDataSalt: 120

sbd_fieldData: 30

sbd_plateauMeasurementFieldData: 30

sbd_plateauSampleFieldData: 30

sdg_externalLabSummaryData: 14
description: Tracer injections of conservative salt are completed 6 times per year to capture a range of flows at NEON wadeable stream sites as part of the wadeable stream reaeration protocol. The first sampling station is located near sensor set #1 and the fourth sampling station is located near sensor set #2. Sampling stations #2 and #3 are approximately evenly spaced between sampling stations #1 and #4. The injection (drip) station is located far enough upstream of sampling station #1 that the tracer is well mixed within the stream channel for all sampling stations. Conductivity data loggers are located near sampling stations #1 and #4 to capture the rising limb and plateau (for constant rate injections) and falling limb (for slug injections) in situ conductivity values. For more information see AOS Protocol and Procedure: Reaeration in Streams [NEON.DOC.000693](http://data.neonscience.org/api/v0/documents/NEON.DOC.000693vH). Instrumentation: YSI Pro2030, HOBO U24
DOI: 10.5281/zenodo.10581321
title: PSTIV3 Historical Occupational Coding system

description: This contains the PSTIV3 coding scheme for historical occupations.The files are described in the Readme file.
DOI: 10.5281/zenodo.10530708
title: Historical sailing routes

description: # Data and scripts for the paper "A multi-criteria simulation of European coastal shipping routes in the ‘age of sail’"


This repository contains all the data and scripts required to fully reproduce all analyses presented in the paper "A multi-criteria simulation of European coastal shipping routes in the ‘age of sail’" authored by Litvine, A.D. Lewis, J. Starzec, A.W.


Getting Started

---------------


1. Open project using Simulating_shipping_routes.Rproj to ensure relative paths work.

2. Run the R scripts in the folder Preprocessing to reproduce the preprocessed data before running the main analysis.

  2.1 wind_uv_preprocessing.R reproduces the aggregated wind U and V raster layers. This function mean aggregates the .nc wind U and V layers for each month. Data is resampled to match the bathymetry dataset

  2.2 currents_uv_preprocessing.R reproduces the aggregated currents U and V raster layers. This function mean aggregates the .nc currents U and V layers for each month. Data is resampled to match the bathymetry dataset

  2.3 calculate_wind_variability.R reproduces the aggregated MoM, CV Speed, and CV Direction raster layers

  2.4 mean_wave_dir_processing.R reproduces the mean wave direction

  2.5 mean_wave_period_processing.R reproduces the mean wave period

  2.6 sig_wave_height_processing.R reproduces the mean significant wave height

  2.7 speed_reduction_processing.R reproduces the speed reduction based on significant wave height and mean wave direction

  2.8 calculate_dir_speed_distributions.R to reproduce plots showing the distribution of wind speed and direction per month

  2.9 dangerous_conditions_1.R to reproduce areas within the study area that have dangerous waves

 

######

 

2.1 Run the 001 2024_01_16_Main.R R script in the R folder to calculate the least-cost paths from all-ports to all-ports for M1, M2, M3, and M3.

2.2 002 2024_01_16_route_lengths.R to calculate the length of each least-cost path for the four models.

2.3 003 2024_01_16_specific_routes.R to calculate the least-cost paths for specific routes (from specific ports) for each of the visibility ranges

2.4 2024_01_16_raster_distributions.R to reproduce the plots showing the spatial distributions of variables
DOI: 10.5281/zenodo.10530709
title: Historical sailing routes

description: # Data and scripts for the paper "A multi-criteria simulation of European coastal shipping routes in the ‘age of sail’"


This repository contains all the data and scripts required to fully reproduce all analyses presented in the paper "A multi-criteria simulation of European coastal shipping routes in the ‘age of sail’" authored by Litvine, A.D. Lewis, J. Starzec, A.W.


Getting Started

---------------


1. Open project using Simulating_shipping_routes.Rproj to ensure relative paths work.

2. Run the R scripts in the folder Preprocessing to reproduce the preprocessed data before running the main analysis.

  2.1 wind_uv_preprocessing.R reproduces the aggregated wind U and V raster layers. This function mean aggregates the .nc wind U and V layers for each month. Data is resampled to match the bathymetry dataset

  2.2 currents_uv_preprocessing.R reproduces the aggregated currents U and V raster layers. This function mean aggregates the .nc currents U and V layers for each month. Data is resampled to match the bathymetry dataset

  2.3 calculate_wind_variability.R reproduces the aggregated MoM, CV Speed, and CV Direction raster layers

  2.4 mean_wave_dir_processing.R reproduces the mean wave direction

  2.5 mean_wave_period_processing.R reproduces the mean wave period

  2.6 sig_wave_height_processing.R reproduces the mean significant wave height

  2.7 speed_reduction_processing.R reproduces the speed reduction based on significant wave height and mean wave direction

  2.8 calculate_dir_speed_distributions.R to reproduce plots showing the distribution of wind speed and direction per month

  2.9 dangerous_conditions_1.R to reproduce areas within the study area that have dangerous waves

 

######

 

2.1 Run the 001 2024_01_16_Main.R R script in the R folder to calculate the least-cost paths from all-ports to all-ports for M1, M2, M3, and M3.

2.2 002 2024_01_16_route_lengths.R to calculate the length of each least-cost path for the four models.

2.3 003 2024_01_16_specific_routes.R to calculate the least-cost paths for specific routes (from specific ports) for each of the visibility ranges

2.4 2024_01_16_raster_distributions.R to reproduce the plots showing the spatial distributions of variables
DOI: 10.48443/dtr7-n376
title: Secchi depth (DP1.20252.001)
title: RELEASE-2024

description: This data product contains the quality-controlled, native sampling resolution data from NEON's Secchi depth data collection. Secchi measurements indicate water clarity, and secchi depth is used to determine the depth to which light penetrates. This value can also be used to calculate the depth of the euphotic zone in a lake or river, which is especially important for phytoplankton sampling. Secchi data are collected when collecting data for any standard operating procedure that samples the water column in a lake or river (e.g., surface water chemistry and phytoplankton) by lowering a Secchi disk through the water column, and recorded the depth(s) to which it disappears from view. Secchi depth measurements are collected only during ice-free periods, and are collected a minimum of 4 times per year, up to 12+ times per year. For additional details, see the user guide, protocols, and science design listed in the Documentation section in this data product's details webpage.

Latency:
The expected time from data and/or sample collection in the field to data publication is as follows, for each of the data tables (in days) in the downloaded data package. See the Data Product User Guide for more information.

dep_secchi: 30
description: Secchi data are collected during sample collection for any standard operating procedure that samples the water column in a lake or river (phytoplankton, zooplankton, pelagic surface water microbes, and pelagic surface water chemistry), and may be collected during other sampling visits to lake and river sites. Measurements are collected only near the buoy sensors in lakes and rivers, and data are not collected under the ice. Secchi depth measurements are only collected during ice-free periods, and are collected a minimum of 4 times per year, up to 12+ times per year. Instrumentation:
DOI: 10.5281/zenodo.10581342
title: Reduction of NQO1 P187S by NADH

description: Raw data published in: Pacheco-Garcia JL, Anoz-Carbonell E, Vankova P, Kannan A, Palomino-Morales R, Mesa-Torres N, Salido E, Man P, Medina M, Naganathan AN, Pey AL. Structural basis of the pleiotropic and specific phenotypic consequences of missense mutations in the multifunctional NAD(P)H:quinone oxidoreductase 1 and their pharmacological rescue. Redox Biol. 2021 Oct;46:102112. doi: 10.1016/j.redox.2021.102112. Epub 2021 Aug 18. PMID: 34537677; PMCID: PMC8455868.

Data measured using a stopped-flow spectrophotometer from Applied Photophysics (SX.18MV, Applied Photophysics Ltd., Leatherhead, UK) interfaced with a photodiode array detector and under anaerobic conditions, following previously established protocols. Multiple wavelength absorption data in the flavin absorption region (400-900 nm) were collected and processed using the ProData-SX software (Applied Photophysics Ltd.). Time-dependent spectral deconvolution was performed by global analysis and numerical integration methods using Pro-Kineticist (Applied Photophysics Ltd.). Collected data were fitted to either single- or multi-step (A→B→n….→Z) models allowing for estimation of the corresponding observed conversion rate constants at each NADH concentration, as well of the spectra of intermediate and final species.

NQO1ox P187S (7.5 μM) was mixed with NADH at concentrations ranging from 1:1 to 1:14 NQO1ox:NADH ratio. Reactions were studied in 20 mM HEPES-KOH, pH 7.4 with glucose/glucose oxidase (310 mM/10 units/mL), at 25 C.

Spectral evolution of NQO1 reductive half-reaction with NADH at different concentrations. Files are numbered from 1 to 7 representing the following NADD concentrations: 7.5, 10, 15, 20, 30, 50 and 100 uM of NADH.