cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.18739/a2b27ps3n
title: Photos of the sea ice surface corresponding to surface albedo datasets collected during the Multidisciplinary drifting Observatory for the Study of Arctic Climate (MOSAiC) campaign in the Central Arctic Ocean, April – September 2020

description: This dataset contains the corresponding photos of the albedo data recorded on the sea ice surface June-September, 2020, during the Multidisciplinary drifting Observatory for the Study of Arctic Climate (MOSAiC) expedition expedition in the Central Arctic Ocean. The corresponding measurements were made in three modes: (i) along ‘albedo lines’, between 60-200 meters (m) in length, with measurements every 5 meters (or 10 meters on leg 3), (ii) at specific ‘library sites,’ or (iii) ‘experiments’. Albedo lines were chosen with the aim of crossing representative surface conditions during the summer sea ice evolution, including snow-covered ridges, bare ice, and ponded ice. Included in the dataset are classification of the surface cover and depth for most measurements. This dataset is collocated with the spectral albedo dataset (doi.org/10.18739/A2FT8DK8Z) and broadband albedo dataset (doi.org/10.18739/A2KK94D36).
DOI: 10.5281/zenodo.3672151
title: Simulation dataset (Project: Spectrum of Public Transit Operations: From Fixed Route to Microtransit)

description: This dataset is generated for the simulation of three different mobility services along the MTA Bus route B63 in Brooklyn, NY. Each includes the information of origin and destination of passengers within the service area and reflects different levels of demand (80, 200, and 400 passenger/hr). The dataset is produced based on MATLAB.
DOI: 10.5281/zenodo.4066768
title: Platon database

description: This repository contains the mandatory pre-built database (db.tar.gz) for Platon (https://github.com/oschwengers/platon). This db version is only compatible with Platon v1.5.0 onwards! This db version is built using RefSeq release 202 containing complete: 20,041 chromosomes 18,795 plasmids
DOI: 10.5281/zenodo.5965773
title: Revisiting the ringdown of GW150914

description: Data release for our publication on "Revisiting the ringdown of GW150914." Released files include posterior samples for all ringdown parameter estimation runs used in the paper. We also include a Jupyter notebook that reproduces plots in the paper from these data (<em>paper_plots.ipynb</em>), as well as a Jupyter notebook that replicates an individual ringdown analysis like those that produced the enclosed parameter estimation results (<em>GW150914_sample_analysis.ipynb</em>). Code associated with this release is also made available through GitHub here.
DOI: 10.6084/m9.figshare.14074499.v1
title: Questionnaire findings - Models of care for CML patients during the COVID-19 pandemic

description: Questionnaire results from our study:"Models of care for Chronic Myeloid Leukaemia (CML) patients during the COVID-19 pandemic in the United Kingdom (UK): changes in patient attitudes to remote consultations and future implications"
DOI: 10.5281/zenodo.3661118
title: Shared mobility opporTunities And challenges foR European citieS (STARS) - Work Package 4

description: These datasets contain data from the Work Package 4 (WP4) in the project STARS. For more information about the project: http://stars-h2020.eu/ <strong>The aims of the WP 4 were: </strong> To study the influence of factors related to individuals and to social settings that can be quantitatively measured; To uncover the role played by different mobility styles and mobility cultures in the diffusion of shared mobility practices; To assess the overall importance of individual, social, political, environmental and economic variables in driving the behavioural change towards shared mobility; To identify barriers and facilitators for a faster shift in life-styles that includes shared mobility.
DOI: 10.5281/zenodo.5528368
title: Simulations of Single Molecule Localization Microscopy frames with scattered single emitters

description: <strong>[THIS IS AN OLD, CLOSED VERSION. PLEASE FIND THE LATEST VERSION HERE: 10.5281/zenodo.5528367]</strong> Datasets used in the work "Combining deep learning with SUPPOSe and Compressed Sensing for SNR-enhanced localization of overlapping emitters". The file <strong>Sample dataset.zip</strong> contains simulated images of frames of Single-Molecule Localization Microscopy. In the directory structure, Q is the number of emitters, d is the emitter distance (in pixels), imax is the image maximum intensity and i indexes different noise realizations. There are three images within each folder: <strong>X</strong> is a noiseless image, <strong>Y</strong> is the image with noise and background and <strong>Z</strong> is a denoised image predicted using a convolutional neural network. The file <strong>Train dataset.zip</strong> contains 5000 simulated pairs of images of single emitters distributed randomly that were used to train a convolutional neural network for denoising. The folder <strong>X</strong> contains noiseless images and the folder <strong>Y</strong> contains the corresponding images with noise and background. In all cases, a Gaussian PSF with size \(\sigma = 3\) px was used as the PSF of the imaging system, Noise is modeled as a Poisson process with a dark signal \(i_{dark} = 10\). Corresponding author: Axel M. Lacapmesure (alacapmesure@fi.uba.ar)
DOI: 10.5281/zenodo.6554513
title: Posterior samples for "Searching for a Ringdown Overtone in GW150914"

description: Posterior files associated with Searching for a Ringdown Overtone in GW150914 (arXiv:2205.07809). We provide samples for both the real GW150914 analysis ("posterior_samples/GW150914") and the injection campaign ("posterior_samples/injection_campaign"). For the GW150914 analysis, where multiple models were used, the folder naming follows the convention: {number of wavelets included in the model}W{QNM content described by lmn indices} with the kerr-deviation analysis having the additional label "_with_deviation". Only the "3W220221" model was used in the injection campaign. There, subfolders are named according to the injection time in seconds (where "m" indicates a minus value, relative to t_ref as detailed in the paper). The exception is the noiseless injection, which is in the "noiseless" folder. Each directory contains a 'posterior_samples.dat' file and a 'sampler_output.json' which contains the log-evidence (natural log) and the estimated error on the log-evidence. Notebooks to reproduce the figures in the paper are available in the "plots" folder.<br>
DOI: 10.6069/44s8-9f68
title: Absolute Protein Quantitation of the Mouse Macrophage Toll-Like Receptor and Chemotaxis Pathways

description: The Toll-like receptor and chemotaxis pathways are key components of the innate immune system. Computational modeling and simulation at the molecular interaction level can be used to study complex biological pathways, but protein concentration values must be input as model parameters. In this investigation, targeted mass spectrometry assays were developed and used to measure the absolute abundance (copies/cell) of proteins of the mouse macrophage Toll-like receptor 4 (TLR4) and chemotaxis pathways. The data produced by this investigation can be used for pathway modeling and simulation, as well as for other systems biology research.
DOI: 10.6073/pasta/d3a70c1f0d534cca8bdebd7f7483ef38
title: Spatiotemporal variation in internal phosphorus loading, sediment characteristics, water column chemistry, and thermal mixing in a hypereutrophic reservoir in southwest Iowa, USA (2019-2020)

description: The primary aim of the data product is to quantify seasonal and spatial variation in sediment phosphorus fluxes in a temperate reservoir and evaluate mechanisms responsible for instances of elevated sediment phosphorus release. We studied Green Valley Lake, a hypereutrophic reservoir in southwest Iowa, USA, from 2019 to 2020. We measured sediment phosphorus flux rates and potential explanatory variables at three sites along the longitudinal gradient of the reservoir over six sampling events during winter and summer stratification as well as mixing events in the spring, summer, and fall. Ex situ sediment core incubations were used to measure sediment P release rates under ambient temperature and dissolved oxygen conditions. Explanatory variables measured included sediment phosphorus chemistry, sediment physical characteristics, epilimnetic and hypolimnetic nutrient concentrations, and thermal stratification patterns. These data will be used to identify mechanisms driving hot spots and hot moments of sediment phosphorus release, which will contribute to our understanding of how areas of lakebed and times of the year can disproportionately influence whole-lake water chemistry.
DOI: 10.6084/m9.figshare.19732849
title: AOsupplemental-documentMinarniDataset1.docx

description: Datasets for reflectance intensities vs wavelengths and fruit firmness
DOI: 10.6084/m9.figshare.19732873
title: AOsupplemental-documentMinarniDataset2.docx

description: Datasets for PCA analysis of oil palm FFBs
DOI: 10.6084/m9.figshare.19732936
title: AOsupplemental-documentMinarni-AdditionalFigures.docx

description: Suplemental Figures of Figure 6 and experimental setups of Figure 1 and 2
DOI: 10.6084/m9.figshare.20462013
title: Supplementary Material for: The More Extensive the Spread through Air Spaces, the Worse the Prognosis Is: Semi-Quantitative Evaluation of Spread through Air Spaces in Pulmonary Adenocarcinomas

description: <b><i>Introduction:</i></b> The extent of spread through air spaces (STAS) is less investigated among patients with lung adenocarcinoma who underwent sublobar resection. Therefore, we aimed to evaluate the extent of STAS semi-quantitatively, to assess its prognostic impact on overall survival (OS) and recurrence-free survival (RFS), and to investigate the reproducibility of this assessment. <b><i>Methods:</i></b> The number of tumour cell clusters and single tumour cells within air spaces was recorded in three different most prominent areas (200x field of view). The extent of STAS was categorized into three groups, and the presence of free tumour cluster (FTC) was recorded. <b><i>Results:</i></b> Sixty-one patients were included. Recurrence was more frequent with higher grade (<i>p</i> = 0.003), presence of lymphovascular invasion (<i>p</i> = 0.027), and presence of STAS of any extent (<i>p</i> = 0.007). In multivariate analysis, presence of FTC (HR: 5.89; 95% CI: 1.63–21.26; <i>p</i> = 0.005) and more pronounced STAS (HR: 7.46; 95% CI: 1.60–34.6; <i>p</i> = 0.01) had adverse impact on OS and RFS, respectively. Concerning reproducibility, excellent agreement was found among STAS parameters (ICC range: 0.92–0.94). <b><i>Discussion:</i></b> More extensive STAS is an unfavourable prognostic factor in adenocarcinomas treated with sublobar resection. As the evaluation of extent of STAS is reproducible, further investigation is required to gather more evidence.
DOI: 10.6084/m9.figshare.5305420
title: Image library: Retrophyllum spiralifolium Wilf, Retrophyllum superstes Wilf, and Retrophyllum araucoensis (Berry) Wilf

description: Full-resolution image library of the three fossil <i>Retrophyllum</i> (Podocarpaceae) species from Argentina and Chile- <i>R. spiralifolium</i> Wilf, <i>R. superstes</i> Wilf, and <i>R. araucoensis</i> (Berry) Wilf - that were published here:Wilf P, MP Donovan, NR Cúneo, MA Gandolfo. 2017. The fossil flip-leaves (<i>Retrophyllum</i>, Podocarpaceae) of southern South America. <i>American Journal of Botany</i>, 104(9), p. 1344-1369, doi: 10.3732/ajb.1700158.Image-file format is:species_specimen number_(photo time stamp).tifAnd for <i>R. spiralifolium:</i>species_specimen number(collection year if after 2002)_ (photo time stamp).tif<br>where the <i>R. spiralifolium</i> specimen number is usually given as locality-field number. Please consult the provided Excel lookup table for the specimen data and formal repository numbers of <i>R. spiralifolium</i> (MPEF-Pb-).Please cite all material by repository number (not field number), prefixes MPEF-Pb, BAR, or USNM.For <i>R. superstes</i>, use the provided scale files (in the zip file) as overlays for microscope photos that lack embedded scales. See the filenames for the magnifications and corresponding microscopes used.<br>Photo time stamp format is usually (YYYYMMDD HHMMSS).Please refer to the primary paper for all details and cite both the primary paper and this Figshare archive if you use these images.As described in the primary paper, fossils of <i>R. spiralifolium</i> from Río Pichileufú are curated at Museo de Paleontología de Bariloche, San Carlos de Bariloche, Río Negro, Argentina (BAR). All other material of <i>R. spiralifolium</i>,<i> </i>and the single specimen of <i>R. superstes</i>, are curated at Museo Paleontológico Egidio Feruglio, Trelew, Chubut, Argentina (MPEF-Pb). The type material of <i>R. araucoensis</i> shown here is housed in the Paleobotanical Division of the National Museum of Natural History, Smithsonian Institution (USNM).Several 'super-resolution' composite images are included. Special thanks to Michael Donovan and Eduardo Ruigomez for assistance with the photography. Contact for any questions: Peter Wilf, pwilf@psu.edu
DOI: 10.6084/m9.figshare.5450602
title: Drosophila 25 species phylogeny

description: We used the peptide sequences for 25 Drosophila species along with an outgroup species, <i>Musca domestica</i>, that were available on NCBI (ftp://ftp.ncbi.nlm.nih.gov/genomes/) and FlyBase (ftp://flybase.net/12_species_analysis/genomes/) as of April 21, 2017. We employed the clustering algorithm MCL to predict orthologous groups of peptides and used the 1,634 ortho-groups that were predicted as being single-copy in all species for phylogeny reconstruction. These groups were aligned with PASTA and the alignments were concatenated and given to RAxML with the PROTGAMMAJTTF model to estimate the species topology and relative branch lengths. Other methods based on individual gene trees (average consensus and ASTRAL) resulted in the exact same topology. We then used r8s to estimate branch lengths in terms of millions of years with three calibration points: 49-59 mya for the common ancestor of <i>D. pseudoobscura</i> and <i>D. melanogaster</i>, 64-74 mya for the common ancestor of <i>D. grimshawi</i> and <i>D. melanogaster</i>, and 156 mya for the common ancestor of <i>D. melanogaster</i> and <i>Musca domestica</i>.<br><br>File summary:<br>1. drosophila-25spec-concordance-factor-tree.png<br>An image of the phylogeny with branches scaled by relative number of substitutions. Nodes are labeled with concordance factors. Concordance factors are calculated for each node in the species phylogeny as: (# of gene trees with that node / total # of gene trees).<br><br>2. drosophila-25spec-node-age-tree.png<br>An image of the phylogeny with branches scaled by millions of years. Nodes are labeled with their ages in millions of years.<br><br>3. drosophila-25spec-time-tree.tre<br>The Newick string of the phylogeny with branches scaled by millions of years. Nodes are labeled with concordance factors.<br><br>4. drosophila-25spec-tree.tre<br>The Newick string of the phylogeny with branches scaled by relative number of substitutions. Nodes are labeled with concordance factors.<br>
DOI: 10.15129/cd4b3d5d-a8c2-4549-a1a5-0fef178ed097
title: Data for: "Ground-state phase diagram of quantum link electrodynamics in (2+1)-d"

description: Data set for "Ground-state phase diagram of quantum link electrodynamics in (2+1)-d" This is a dataset which contains the csv files of the data points and simplified scripts that are needed for recreating the figures : 3a, 3b, 3c, 3d, 4, 5a, 5b, 5c, 5s, 6, 7, 8, 9, 10, 11a, 11b, 11c, 11d, 12a, 12b, 12c, 13a, 13b, 13c, 13d, 13e, 13f, that are produced by Tomohiro Hashizume (University of Strathclyde) in the Journal Article *Ground-state phase diagram of quantum link electrodynamics in (2+1)-d* accepted in SciPost Physics on 4 July 2022. ## Folder `main`: * Folder `data` contains folders named `FIG_#`, which contain the data points of the relevant Figures in the **main text**. Please replace `#` with the relevant figure number. * Folder `scripts` contains small scripts which recreates the simplified versions of the relevant figures. ## Folder `appendix`: * Folder `data` contains folders named `FIGAPP_#`, which contain the data points of the relevant Figures in the **Appendix**. Please replace `#` with the relevant figure number. * Folder `scripts` contains small scripts which recreates the simplified versions of the relevant figures. For the details, please refer to the individual README files within the folders. Any known constants that are plotted, are mentioned in the published text and they are also hard coded in the scripts in this dataset.
DOI: 10.5281/zenodo.5791855
title: Mapping 10-m global impervious surface area (GISA-10m) using multi-source geospatial data

description: Artificial impervious surface area (ISA) documents human footprints. Accurate, timely, and detailed ISA datasets are therefore essential for global climate change and urban planning. However, due to the lack of sufficient training samples and operational mapping methods, global ISA mapping at 10-m resolution is still lacking. To this end, we proposed a global ISA mapping method leveraging multi-source geospatial data. Based on the existing satellite-derived ISA maps and the crowdsourcing OpenStreetMap (OSM), 58 million training samples were extracted via a series of temporal, spatial, spectral, and geometric rules. Combined with over 2.7 million Sentinel optical and radar images on the Google Earth Engine, we produced the 10 m global ISA dataset (GISA-10m). Based on the test samples that are independent to the training set, GISA-10m embraced an overall accuracy greater than 86%. In addition, the GISA-10m was comprehensively compared with the existing global ISA datasets, and the superiority of GISA-10m was demonstrated. The global dataset can be interpreted using the vrt file provided (GISA-10m_v01_2016.vrt).
DOI: 10.5281/zenodo.6361712
title: 3D ED tilt series of Argyrin D

description: The electron diffraction tilt series (3D ED) was collected in continuous rotation mode using the dedicated TEM-controlling script (Gorelik at al., 2021). The sample was ultrasonically dispersed in EtOH. A drop of the suspension was placed onto carbon-coated TEM cupper grid. 3D ED data were collected using a Thermofischer TALOS TEM, operated at 200kV (Ulm University). The data were collected at liquid nitrogen temperature. Dry sample was inserted into the TEM and then cooled – no cryo-transfer procedure was applied. Cryo-transfer sample holder allowing for high-tilt goniometer rotation was used. Electron diffraction was performed in nanodiffraction mode with condenser C2 aperture of 50 microns. The effective beam diameter on the sample was about 7 microns. The sample was scanned with the electron dose rate of 0.003 e/A2s, electron diffraction patterns were collected with the dose rate of 0.03 e/A2s. A single dataset within a tilt range of -70…70° containing 118 frames, had a total accumulated dose of 3.5 e/A2. Binning 4 of the CETA camera was used, camera length was 1.35m, resulting in the pixel size of 0.00166 A-1 of 1024x1024 frames, corresponding to the effective detector distance of 1,344 mm. Single frame exposure was 1 second, relative goniometer rotation speed 0.04, resulting in the effective oscillation range of 1.18°. The lateral crystal size was ca. 1.5 micron x 6 micron. <em>Gorelik et al., 2021. Acta Cryst. B77, 662–675.</em>
DOI: 10.6084/m9.figshare.16755514
title: Data for "In vitro and in vivo NIR Fluorescence Lifetime Imaging with a time-gated SPAD camera"

description: Data, analysis scripts and logs
DOI: 10.6084/m9.figshare.17209610
title: lct_corpus.tar.gz

description: The Leaf Clinical Trials (LCT) corpus: an annotated corpus of clinical trials eligibility criteria.<br>
DOI: 10.5281/zenodo.6573989
title: Extract from the PEAPL framework : Modelling "Writing sentences" competency (French as the schooling language)

description: Competences, skills and knowledges that make up "writing sentences" competency, based on the linguistic praxeological organization of French as the schooling language (https://doi.org/10.5281/zenodo.4001381). This is an extract of the general framework, some of the visible objects are linked to other objects in other main competences. Orange links show how pedagogic ressources (game levels) are linked to framework objects. This framework is used for the PEAPL (peapl.eu) project to link activities in the GamesHub platform (for example activities using "L'Orthodyssée des Gram" grammar online game, available at https://www.lafamillegram.ch/#)
description: PEAPL project Project reference : 2020-1-FR01-KA201-080620 EU grant : 449923 EUR
DOI: 10.21227/b2k0-pb76
title: Nifty-50 Companies

description: This data set contains nifty 50 companies and all their details of Open, Volume, Close, Adj Close, and name of the company.
DOI: 10.25326/10
title: Standard daily IASI/Metop-A ULB-LATMOS ammonia (NH3) L2 product (total column)

description: The standard IASI/Metop-A daily ammonia (NH3) total column dataset (ANNI-NH3-v2.2), described in [Van Damme et al.](https://www.atmos-meas-tech.net/10/4905/2017/) (2017) includes the results of a flexible and robust NH3 retrieval algorithm from measurements of the Infrared Atmospheric Sounding Interferometer (IASI). The method is based on the calculation of a spectral hyperspectral range index (HRI) and subsequent conversion to NH3 columns via a neural network. With this method: (1) complete temperature and humidity vertical profiles can be accounted for, (2) third‐party NH3 vertical profile information can be used, and (3) a full measurement uncertainty characterization is provided. Separate neural networks were trained for land and sea observations. Recommendations for post-filtering the data and for averaging data in time or space are formulated in [Van Damme et al.](https://www.atmos-meas-tech.net/10/4905/2017/) (2017). ANNI-NH3-v2.2 relies on near real time meteorological parameters provided by Eumetsat (L2 data from IASI PPF). The dataset is available on a global scale from October 2007 till December 2017.

Current Version: V2.2.0, available since 2018-06-15

 - The main change from V2.1.0 to V2.2.0 is a first-order correction that had to be applied on the entire HRI/Metop-B time-series and on HRI/Metop-A after 7 June 2017 due to a change in the Level 1 information treatment in 2017 for Metop-A. 

Version history: V2.1.0, available from 2017-09-30 to 2018-06-15

Disclaimer: The Eumetsat IASI PPF L2 data processing chain has been updated several times since IASI launch, inducing discontinuities in the retrieved NH3 time-series. A second dataset (ANNI-NH3-v2.2R-I) which relies on ERA-Interim ECMWF meteorological input data, along with surface temperature retrieved from a dedicated network, rather than the operationally provided Eumetsat IASI Level 2 (L2) data used for the standard version is also available on AERIS Website [NH3_R-I](https://en.aeris-data.fr/metadata/?871d9366-22d7-4d8d-997e-02e7721f7e94). For inter-annual comparisons and trends analyses, only the reanalysed dataset should be used.
DOI: 10.25919/1va2-h045
title: GASKAP-HI Pilot Survey Science - Small Magellanic Cloud HI absorption spectra

description: This dataset contains HI absorption spectra towards 373 continuum sources in the region of the Small Magellanic Cloud (SMC). These were produced by the GASKAP HI Absorption Pipeline from 20 hours of ASKAP pilot observations of the SMC. The accompanying catalogues describe the 229 spectra that satisfied the quality requirements for analysis along with the 122 absorption features identified in those spectra.