cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17040/iscn/1346192
title: Blodgett Forest Warming Experiment 1

description: Carbon stocks and density fractions from soil pits used to characterize soils of the Blodgett warming experiment as well as gas well CO2, 13C, and 14C data from experimental plots. The experiment consisted of 3 control and heated plot pairs. The heated plots are warmed +4°C above the control from 10 to 100 cm.
DOI: 10.24356/sd/20/9
title: Military Diplomacy and Its Present Functions

description: Military diplomacy can be defined as a set of activities carried out mainly by the representatives of the defence department, as well as other state institutions, aimed at pursuing the foreign policy interests of the state in the field of security and defence policy, and whose actions are based on the use of negotiations and other diplomatic instruments. This meaning differs military diplomacy from some other related phenomena such as gunboat diplomacy or coercive diplomacy. Military diplomacy as such performs several basic functions, which include the following: 1. Gathering and analysing of information on the armed forces and the security situation in the receiving state, 2. Promotion of cooperation, communication and mutual relations between the armed forces of the sending and the receiving state, 3. Organization of working visits of representatives of the defence authorities and of peaceful stay of the military units of the sending state in the receiving state, 4. Support of business contracts with arms and military equipment between the sending and the receiving state, and 5. Representation of the sending state and its armed forces at official ceremonies and other events in the receiving state.
DOI: 10.25318/2510001501-eng
title: Electric power generation, monthly generation by type of electricity

description: Electricity generation by class of electricity producer (electric utilities, electricity producers, industries, etc.) and type of electricity generation (hydroelectric, combustible fuels, wind, etc.). Data are presented at the national and provincial levels, however not all combinations are available.
DOI: 10.25318/3310022201-eng
title: Canadian Business Counts, with employees, December 2019

description: Canadian Business Counts, location counts with employees, by employment size ranges and North American Industry Classification System (NAICS), Canada and provinces, December 2019.
DOI: 10.25345/c5ft8dw1z
title: MassIVE MSV000093480 - Shedding Light on the Elusive Dark Ig-Ome: Elucidating and Profiling Neutralizing Antibodies Derived from Human Plasma Post SARS - CoV - 2 Vaccination through a d e Novo Sequencing Proteomics and B - cell Repertoire Analysis
title: We are submitting raw data files used for de novo sequencing of human polyclonal antibodies targeting receptor binding domain (RBD) from covid-19 virus to generate recombinantly produced monoclonal antibodies capable of neutralizing RBD. The raw files submitted are described in the metafile included, but in brief, they are categorized as data generation (i.e., bottom-up in-solution enzymatic digestion), native gel separation followed by digestion, non-reducing room temperature (NRT) gel separation followed by digestion, middle-down, non-reducing, and isobaric resolution.
DOI: 10.25405/data.ncl.22144442
title: Data used for the validation of the BIONICS research embankment hydromechanical model

description: <strong>Summary</strong> This archive contains the data used to produce a number of the figures in the linked Morsy <em>et al.</em> (2023) publication. The linked repository consists of: Deformation data used in the embankment model validation Data on the embankment foundation along with the fill density and porosity Undrained triaxial test data used for validation of the strain-softening model <em>In-situ</em> and modelled soil water retention behaviour of the embankment fill Meteorological data related to evapotranspiration Modelled and field monitored time series of slope pore water pressures and water content Modelled and monitored embankment settlement data Modelled slope surface deformations. <strong>Further Information:</strong> The research work was funded by the ACHILLES project (EPSRC programme grant EP/R034575/1). The data from the BIONICS embankment used in the model validation was also produced as part of the EPSRC funded BIONICS (GR/S87430/01) and iSMART (EP/K027050/1) projects. For more information, please visit the ACHILLES project website. Field data used in this work is available from the linked dataset in the reference section.
DOI: 10.26302/sshade/experiment_lb_20231006_001
title: Vis-NIR reflectance spectra (i = 0°, e = 30°) of three raw chips of the Orgueil CI chondrite under ambient conditions

description: Vis-NIR reflectance spectra (i = 0°, e = 30°) of 3 different raw chips of the Orgueil CI chondrite (having being stored in distinct conditions) under ambient conditions
DOI: 10.34808/t9a7-yz17
title: Floating treatment wetland with Equisetum hyemale - performance in nutrients and potentially toxic elements removal

description: This data set contains the results of a microcosm experiment with floating treatment wetlands (FTW) conducted under artificial conditions. The goal of this experiment was to determine the effect of stress factors (Pb, As, increased salinity) on the nutrient uptake capacity of Equisetum hyemale in FTW. The ability of E.hyemale to uptake Pb and As was also investigated. 
This data set contains the results of physiochemical parameters of treatments as well as the plants' characteristics throughout the experiment. Mass balance calculations for Pb and As are also included.
The entire experiment lasted 50 days, from March 1 to April 21, 2021. The experiment was divided into two phases: the first lasted 30 days, and the second lasted 20 days.
DOI: 10.48480/x293-8050
title: Factsheets for bio-based carbon dioxide removal options in Germany
DOI: 10.5281/zenodo.10469322
title: Polarisation camera movie of single SYTOX Orange molecules on a cover glass

description: This image dataset is a movie of the fluorescence of single SYTOX Orange molecules (S34861, Invitrogen) dispersed on a cover glass. The data was collected on a fluorescence microscope (Ti-U, Nikon) with a polarisation camera (CS505MUP, Thorlabs). The molecules were excited with a 532 nm diode laser with a measured power density at the sample plane of 0.36 kW/cm^2. An exposure time of 100 ms was used. The following filters were used: dichroic (Di03-R532-t1, Semrock) and emission filter (FF01-582/64, Semrock).
DOI: 10.5281/zenodo.10469445
title: Polarisation camera PAINT movie of single Nile red dyes binding to lipid bilayer-coated silica microspheres

description: This PAINT dataset is a movie of the fluorescence of single Nile red molecules reversibly binding to a lipid bilayer (DPPC + 40% cholesterol) on a 5 μm diameter silica microsphere (44054-5ML-F, Sigma-Aldrich). Images were recorded at 3 different focal planes; approximately at the midpoint of the bead (z1), the top of the bead (z3) and a position in between (z2).

The data was collected on a fluorescence microscope (Eclipse Ti2, Nikon) with a polarisation camera (CS505MUP, Thorlabs). The molecules were excited with a 514 nm DPSS laser with a measured power density at the sample plane of 6.08 kW/cm^2. An exposure time of 50 ms was used. The following filters were used: dichroic (Di03-R514-t1, Semrock) and emission filter (FF01-515/LP and FF01-650/200, Semrock).
DOI: 10.5281/zenodo.10470795
title: Polarisation camera TAB-PAINT dataset of alpha-synuclein fibrils using Nile red

description: Alpha-synuclein fibrils were deposited on PLL-coated and argon plasma-cleaned coverslides. A low concentration of Nile Red (~1 nM) was added for PAINT imaging, and fluorescent beads for post-acquisition drift correction.

The data was collected on a fluorescence microscope (Eclipse Ti-U, Nikon) with a polarisation camera (CS505MUP, Thorlabs). The molecules were excited with a 515 nm laser using epi-illumination with a measured power density at the sample plane of 6.08 kW/cm^2. An exposure time of 50 ms was used. The following filters were used: dichroic (Di03-R514-t1, Semrock) and emission filter (FF01-515/LP and FF01-650/200, Semrock). A 60x oil-immersion objective (Plan Apo, 60xA/1.40 Oil, DIC H, inf/0.17 WD 0.21, Nikon) was used for detection.
DOI: 10.5281/zenodo.10470982
title: Polarisation camera dSTORM datasets of actin in fixed HeLa cells labeled with phalloidin-Alexa Fluor 488

description: Polarisation camera dSTORM dataset of the actin of fixed HeLa cells labeled with phalloidin-Alexa Fluor 488.

Image acquisition was performed as follows:

Imaging was performed on a widefield microscope equipped with a polarisation camera (CS505MUP, Thorlabs). The sample was excited using a 488 nm laser at quasi-TIRF, with a measured power density at the image plane of 5.04 kW/cm^2. A single long-pass dichroic (Di02-R488, Semrock) was used to seperate fluorescence from the excitation. The emission was filtered using a long-pass (BLP01-488R, Semrock) and a bandpass filter (FF01-582/64, Semrock) before detection. An exposure time of 30 ms was used.

Samples were prepared as follows:

Cell culture: HeLa TDS cells were cultured in DMEM (Gibco, Invitrogen) supplemented with 10 % Fetal Bovine Serum (FBS, Life Technologies), 1 % penicillin/streptomycin (Life Technologies), and 1 % glutamine (Life Technologies) at 37 °C + 5 % CO_2. Cells were periodically tested for mycoplasma contamination and passaged 3 times per week. Cells were plated at low density on high-precision glass coverslips (MatTek, P35G-0.170-14-C) 1 day prior to fixation for dSTORM experiments.

Labeling: Cells were simultaneously fixed and permeabilized in cytoskeleton buffer (CBS, 10 mM MES, 138 mM KCl, 3 mM MgCl_2, 2 mM EGTA, 4.5 % sucrose w/v, pH 7.4), + 4 % paraformaldehyde (PFA) and 0.2 % Triton for 6 minutes at 37 °C, and further fixed in CBS + 4 % PFA for 14 minutes at 37 °C. Post-fixation, cells were washed x3 in PBST (PBS supplemented with 0.1 % Tween) and permeabilized a second time in PBS + 0.5 % Triton for 5 minutes at room temperature. The samples were then washed 3 times in PBST and blocked for 30 minutes in 5 % BSA. Cells were washed x3 in PBST and then incubated with Alexa Fluor™ 488 Phalloidin (A12379, Invitrogen, 1:50 in PBS) for 1 h in the dark, followed by x2 washes in PBS. Prior to dSTORM imaging, PBS was replaced with dSTORM imaging buffer (base buffer consisting of 0.56 M glucose, 50 mM Tris (pH 8.5), and 10 mM NaCl supplemented with 5 U/mL pyranose oxidase (Sigma, P4234), 10 mM cysteamine (Sigma, 30070), 40 µg/mL catalase (Sigma, C100) and 2 mM cyclooctatetraene (Sigma, 138924).
DOI: 10.5281/zenodo.10471496
title: Polarisation camera movies of T cells on a cover glass

description: The plasma membrane of live T cells (J8 LFA-1) was labelled using the Nile red-derivative NR4A, and 3D movies were recorded using a polarisation camera. Two unprocessed datasets are included here:



Tcell_NR4A_EPI_stack: A 3D stack of a single T cell, imaged with the excitation in EPI configuration.

Tcell_NR4A_HILO_stack_movie: A 3D movie of live T cells interacting with an OKT3 antibody-coated cover glass, imaged with the excitation in HILO configuration.


For each .tif file, the corresponding Micro-Manager metadata file is included.

Optical setup:

Imaging was performed on a widefield microscope equipped with a polarisation camera (CS505MUP, Thorlabs). The sample was excited using a 515 nm laser, coupled into a square-core multi-mode fiber (M97L02, Thorlabs) with a custom vibration-motor-based mode scrambler. The measured power density at the image plane was on the order of 0.004 kW/cm^2. A dichroic (Di03-R514-t1, Semrock) was used to seperate fluorescence from the excitation. The emission was filtered using a long-pass filter (FF01-515/LP, Semrock) and bandpass filter (FF01-650/200, Semrock) before detection.

Sample preparation:

J8 LFA-1 cells were incubated overnight (~18 h) in complete-RPMI (StableCell RPMI-1640 media (Sigma) supplemented with 10 % (v/v) fetal calf serum (FCS), 1 % (v/v) HEPES buffer, and 1 % (v/v) pen/strep antibiotics. 1 mL of cells were collected by centrifugation and resuspended in phenol-red free RPMI supplemented with 1 % HEPES.

Round coverslips were rinsed with IPA, MilliQ, dried, and Ar-plasma cleaned for 20 minutes. Grace Bio-Labs CultureWells were attached, and the slide was incubated with OKT3 antibody (provided by the Human Immunology Unit, WIMM, Oxford) for 30 minutes. The slide was washed 5 times with phenol-red free RPMI supplemented with 1 % HEPES and a final wash with phenol-red free RPMI supplemented with 1 % HEPES and 200 nM NR4A before imaging.
DOI: 10.5281/zenodo.10578308
title: Pixel-dependent offset, gain, variance and readnoise maps for CS505MUP polarisation camera

description: These four tif files are the pixel-dependent camera offset (in ADU counts), gain (in ADU counts/photoelectron), variance (in ADU counts^2) and readout noise (in photoelectrons) for the full sensor of a polarization camera (CS505MUP, Thorlabs), as measured using the camera calibration method described in the Supplementary material of the following paper:



Huang, F., Hartwich, T., Rivera-Molina, F. et al. Video-rate nanoscopy using sCMOS camera–specific single-molecule localization algorithms. Nat Methods 10, 653–658 (2013). https://doi.org/10.1038/nmeth.2488
DOI: 10.5281/zenodo.10732697
title: Polarisation camera dSTORM datasets of actin in fixed HeLa cells labeled with phalloidin-Alexa Fluor 647

description: Polarisation camera dSTORM dataset of the actin of fixed HeLa cells labeled with phalloidin-Alexa Fluor 647.

Image acquisition was performed as follows:

Imaging was performed on a widefield microscope equipped with a polarisation camera (CS505MUP, Thorlabs). The sample was excited using a 638 nm laser at quasi-TIRF, with a measured power density at the image plane of 3.51 kW/cm^2. A multiband dichroic (Di03-R405/488/561/635-t1, Semrock) was used to seperate fluorescence from the excitation. The emission was filtered using a long-pass filter (BLP01-635R, Semrock) before detection. An exposure time of 30 ms was used.

Samples were prepared as follows:

Cell culture: HeLa TDS cells were cultured in DMEM (Gibco, Invitrogen) supplemented with 10 % Fetal Bovine Serum (FBS, Life Technologies), 1 % penicillin/streptomycin (Life Technologies), and 1 % glutamine (Life Technologies) at 37 °C + 5 % CO_2. Cells were periodically tested for mycoplasma contamination and passaged 3 times per week. Cells were plated at low density on high-precision glass coverslips (MatTek, P35G-0.170-14-C) 1 day prior to fixation for dSTORM experiments.

Labeling: Cells were simultaneously fixed and permeabilized in cytoskeleton buffer (CBS, 10 mM MES, 138 mM KCl, 3 mM MgCl_2, 2 mM EGTA, 4.5 % sucrose w/v, pH 7.4), + 4 % paraformaldehyde (PFA) and 0.2 % Triton for 6 minutes at 37 °C, and further fixed in CBS + 4 % PFA for 14 minutes at 37 °C. Post-fixation, cells were washed x3 in PBST (PBS supplemented with 0.1 % Tween) and permeabilized a second time in PBS + 0.5 % Triton for 5 minutes at room temperature. The samples were then washed 3 times in PBST and blocked for 30 minutes in 5 % BSA. Cells were washed x3 in PBST and then incubated with Alexa Fluor™ 647 Phalloidin (A22287, Invitrogen, 1:50 in PBS) for 1 h in the dark, followed by x2 washes in PBS. Prior to dSTORM imaging, PBS was replaced with dSTORM imaging buffer (base buffer consisting of 0.56 M glucose, 50 mM Tris (pH 8.5), and 10 mM NaCl supplemented with 5 U/mL pyranose oxidase (Sigma, P4234), 10 mM cysteamine (Sigma, 30070), 40 µg/mL catalase (Sigma, C100) and 2 mM cyclooctatetraene (Sigma, 138924).
DOI: 10.5281/zenodo.10756554
title: Hydrodynamics mediates biogeochemical dynamics of particulate organic matter in the shelf of the northern South China Sea during summer
DOI: 10.5281/zenodo.10867171
title: NanoVarBench variant truthset files

description: These tarballs contain the variant truthsets used for each sample in our paper "Benchmarking reveals superiority of deep learning variant callers on bacterial nanopore sequence data".

Each directory contains the following files:



 <sample>.bed - A BED file of all regions in the genome

<sample>.repetitive_regions.bed - A BED file of all repetitive regions of the genome (see the paper for details of how these were identified).

<sample>.unique_regions.bed - Non-repetitive regions of the genome. This is the result of performing bedtools complement -i <repetitive BED> -g <faidx of mutref>

ani.tsv - skani output from skani search for the sample's assembly against all of the downloaded genomes for that species. The last three columns are not from skani. They are completeness_percentile, completeness, and contamination metrics, all obtained from NBCI for each assembly accession.

apply.vcf.gz - the variants that were applied to the sample's reference assembly.

apply.vcf.gz.csi - VCF index for the above VCF

dnadiff.vcf.gz - Variants between the sample and donor genome from mummer4

minimap2.vcf.gz - Variants between the sample and donor genome from minimap2

mutdonor.fna - the FASTA file of the selected variant donor

mutreference.fna - the sample's reference assembly with the apply.vcf.gz applied to it. This is the genome that the sample's read are aligned to for calling variants

mutreference.fna.fai - the faidx of the above genome

reference.fna - the reference assembly of the sample. These are also available on GenBank, but are included here for interoperability

truth.vcf.gz - the truthset of variants. This is essentially apply.vcf.gz with the REF and ALT invert and the POS adjusted for the difference in position between the sample and donor assemblies. (See this script)

vcfstats.txt - VCF statistics produced by paftools.js vcfstat on the truth VCF


For information about each sample, refer to the samplesheet and paper.
DOI: 10.5281/zenodo.11107198
title: Data for: Redshift Prediction with Images for Cosmology using a Bayesian Convolutional Neural Network with Conformal Predictions

description: These files contain the predictions from the CNN and BCNN model from the paper titled: "Redshift Prediction with Images for Cosmology using a Bayesian Convolutional Neural Network with Conformal Predictions" (Jones et al. 2024). These files will allow reproduction of the performance metrics described in the paper.

 

full_prediction_set_CNN.csv - predictions for the redshift using    the CNN    model of the entire datasetcnn_evaluation.csv - predictions from just the evaluation dataset that was not used in training

Columns are:

photoz - predicted photoz from the modelspecz  - spectroscopic redshiftobjectid - object ID from HSC PDR2 data release (Aihara et al. 2019)

full_prediction_set_BCNN.csv - predictions for the redshift using the BCNN model of the    entire datasetbcnn_evaluation.csv - predictions from just the evaluation dataset that was not used in training

Columns are:

photoz - predicted photoz from the modelspecz  - spectroscopic redshiftobjectid - object ID from HSC PDR2 data release (Aihara et al. 2019)photoz_uncertainty - uncertainty in the    predicted photoz
DOI: 10.5281/zenodo.13208305
title: IAS2024 coastal sea level dataset

description: A new dedicated coastal sea level dataset called International Altimetry Service 2024 (IAS2024) for monitoring sea level changes along the world’s coastlines has been presented. The 'track' folder contains the Monthly sea level anomaly (SLA) time series at 20-Hz along-track points for different ground track segments from Jason missions over global coastal oceans, while the 'virtual' folder contains the SLA time series at three sets of altimeter-based virtual stations along the world's coastlines. These three sets of virtual stations are named as onshore, nearshore and offshore virtual stations, which are derived over 0-10 km, 5-15 km and 10-20 km coastal strips. Note that the above datasets can be used to monitor the coastal sea level changes and to investigate the spatial variation of sea level from offshore towards the coast.
DOI: 10.5281/zenodo.3994953
title: SeaFlow data v1: High-resolution abundance, size and biomass of small phytoplankton in the North Pacific

description: The data set consists of SeaFlow-based cell abundance, cell size (equivalent spherical diameter) and carbon biomass for picophytoplankton populations, namely the cyanobacteria Prochlorococcus, Synechococcus and small-sized Crocosphaera (2-5 um), and picoeukayotes phytoplankton and nanophytoplankton (2-5 μm ESD). SeaFlow is an underway flow cytometer that provides continuous shipboard observations of the optical properties of the smallest phytoplankton. The instrument collects the equivalent of 1 sample every 3 minutes or every 1 km (for a ship moving at 10 knots) from the ship’s flow-through seawater system. Since 2010, the instrument has been operated for 14,000 hours across 140,000 km of ocean, collecting over 300,000 samples in surface waters. Further information can be found on the SeaFlow website SeaFlow_allstats_vX,X_DATE.zip: contains SeaFlow data for each individual cruise, as described in Ribalet et al. (2019). SeaFlow_cmap_vX.X_DATE.xlsx: contains only "best" estimates of SeaFlow data, formatted for Simons CMAP datase.
description: This work was supported by grants from the Simons Foundation (#574495 to FR, #329108 to EVA and AEW, and #426570SP and #549894 to EVA), the Gordon and Betty Moore Foundation (#3776 to EVA) and the National Aeronautics and Space Administration (#80NSSC17K0561 to FR)
DOI: 10.5281/zenodo.4647893
title: Twitter dataset - Coordinated Behavior on Social Media in 2019 UK General Election

description: This dataset contains ~11M tweets related to the 2019 United Kingdom General Election, published and collected between November 12, 2019, and December 12, 2019. In addition, we provide nodes and edges of the superspreader user similarity network, as described in the paper below. Please, refer to the paper below for more details. <strong>Nizzoli, L., Tardelli, S., Avvenuti, M., Cresci, S., & Tesconi, M. (2021). Coordinated Behavior on Social Media in 2019 UK General Election. In 15th International Conference on Web and Social Media. AAAI.</strong> In detail, the dataset consists of: <em>tweet-ids.csv.zip</em>: a CSV file with the column "tweet_id," containing 11,264,820 tweet IDs related to the 2019 United Kingdom General Election, published and collected between November 12, 2019, and December 12, 2019. <em>superspreader-nodes.csv.zip</em>: a CSV file with the columns "id" and "cluster," relating to the nodes of the superspreader user similarity network mentioned in the paper. <em>superspreader-edges.csv.zip</em>: a CSV file with the columns "source," "target," and "weight," relating to the edges of the superspreader user similarity network mentioned in the paper.
DOI: 10.5281/zenodo.5528827
title: Photometric Redshifts for Cosmology: Improving accuracy and uncertainty estimates using Bayesian Neural Networks

description: This data consists of  286,401 with broad-band g,r,i,z,y photometry from the HSC DR2 survey and spectroscopic redshifts.  The majority of galaxies in our sample lies between redshift of 0.01 and 2.5
DOI: 10.5281/zenodo.7939884
title: Exploring global data sets to detect changes in soil microbial carbon and nitrogen over three decades