cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4560862.v2
title: Transcriptome - Nutomonas longa

description: <i>Nutomonas longa</i>'s transcriptome<i> </i>(formerly known as <i>Planomonas carolina)</i><br><br>- clean.fasta: Assembly cleaned from cross-contamination of other species multiplexed (Corallochytrium limacisporum India, Ichthyophonus hoferi and Sphaerothecum destruens) after applying CroCo V0.1.1 (Simion et al. in prep).<br>- Assembly in-home BGI to obtain Unigene (contigs)- ORF prediction using TransDecoder (Trinity plugin) and PfamScan to obtain coding sequences (CDS files) from transcripts (mRNA)- Protein translations are included (pep)<br><strong>Guifré Torruella, Alex de Mendoza, Xavier Grau-Bové, Meritxell Antó, </strong>Mark A. Chaplin<strong>, Javier del Campo, </strong>Laura Eme, Gregorio Pérez-Cordón, Christopher M. Whipps, Krista M. Nichols, Richard Paley, Andrew J. Roger, Ariadna Sitjà-Bobadilla, Stuart Donachie,<strong> and Iñaki Ruiz-Trillo. </strong>(2015)<br><em>Phylogenomics reveals convergent evolution of lifestyles in close relatives of animals and fungi.</em><br><strong><em>Current Biology </em></strong>25(18):2404-10.<br><br>www.multicellgenome.com
DOI: 10.25828/v2ky-v879
title: Quality of Life Survey 2023-2024, Round 7
DOI: 10.21227/kg94-0z57
title: Bitcoin Consensus Changes

description: The dataset contains development archives of more or less interesting conversations, announcements, discussions, presentations and so on regarding consensus changes in Bitcoin.
DOI: 10.18164/e73c7f47-df9c-4877-923c-20e09db28176
title: Major Ions and Acidifying Gases
title: Ions principaux et gaz acidifiants

description: Ambient air is sampled daily, with a nominal 24-hour sampling period, on a Canadian Air and Precipitation Monitoring Network (CAPMoN) sequential sample head located 10 meters above ground. Air is drawn through a three-stage filter pack consisting of 47-millimeter Teflon, nylon and cellulose filters. Particulate Cl-, NO3-, SO4=, NH4+, Na+, K+, Ca++ and Mg++ are collected on the Teflon filter, gaseous HNO3 and a small amount of SO2 are collected by the nylon filter, and gaseous SO2 and residual HNO3 are collected by the K2CO3-impregnated cellulose filter. Filter loadings determined by laboratory extraction and analysis are blank corrected and divided by calibrated sample air volume to get atmospheric concentration in micrograms per cubic meter at International Union of Pure and Applied Chemistry (IUPAC) standard temperature and pressure. The sampling and analysis methodology is described in Sirois and Fricke, 1992.
description: Un échantillon d’air ambiant est prélevé quotidiennement, sur une période d’échantillonnage nominale de 24 heures, à l’aide d’une tête d’échantillonnage séquentielle du Réseau canadien d’échantillonnage des précipitations et de l’air (RCEPA) située à 10 mètres au-dessus du sol. L’air est aspiré à travers un ensemble de trois filtres, en téflon, en nylon et en cellulose, d’une épaisseur totale de 47 millimètres. Les ions Cl-, NO3-, SO4=, NH4+, Na+, K+, Ca++ et Mg++ sont recueillis sur le filtre en téflon, le HNO3 gazeux et une petite quantité de SO2 le sont par le filtre en nylon, et le SO2 gazeux et le HNO3 résiduel, par le filtre en cellulose imprégné de K2CO3. Les charges des filtres, déterminées par l’extraction et l’analyse en laboratoire contre un blanc, sont divisées par le volume d’air de l’échantillon étalonné pour l’obtention de la concentration atmosphérique en microgrammes par mètre cube, à la température et à la pression normales établies par l’Union internationale de chimie pure et appliquée (UICPA). Les méthodes de prélèvement et d’analyse sont décrites dans Sirois et Fricke, 1992.
DOI: 10.21335/nmdc-350572235
title: Seabed sediment data (upper 6 cm) on water content, total nitrogen, total carbon, total organic carbon, total inorganic carbon, carbon and nitrogen isotopic composition from the Nansen Legacy seasonal cruise 2021704 (Q2).

description: This dataset includes contents of water content, total nitrogen (TN), total carbon (TC), total organic carbon (TOC), total inorganic carbon (TIC), and carbon and nitrogen isotopic composition (d13C, d15N) in marine sediments. Samples were collected during the Nansen Legacy cruises in March as part of cruise 2021704 (Q2) in the northern Barents Sea. Sediment material was subsampled from three replicate deployments of a giant box corer at five stations (P1 to P7). The samples were immediately sliced into 1 cm layers (0 - 6 cm) and placed into plastic jars, and frozen on board. All samples were freeze-dried under vacuum in the laboratory and homogenized. Elemental analysis of carbon and nitrogen concentrations was undertaken with an Elemental Analyser - Isotope Ratio Mass Spectrometry (EA - IRMS; Iso ‐ Analytical Ltd., UK). Before d13C analysis, samples were acidified with 1M HCl and left overnight to allow the inorganic carbon to be liberated as CO2. The samples were then neutralized by repetitively washing with distilled water and oven drying at 60 degrees Celsius. The standards d13CV-PDB (Vienna PeeDee Belemnite) and d15NAIR (atmospheric N2) were used as references for the carbon and nitrogen isotope values, respectively. The measured TOC content was corrected for weight loss upon acid washing, TIC content was calculated by subtracting TOC from TC.
DOI: 10.21335/nmdc-799257283
title: Seabed sediment data (upper 6 cm) on water content, total nitrogen, total carbon, total organic carbon, total inorganic carbon, carbon and nitrogen isotopic composition from the Nansen Legacy seasonal cruise 2019711 (Q4).

description: This dataset includes contents of water content, total nitrogen (TN), total carbon (TC), total organic carbon (TOC), total inorganic carbon (TIC), and carbon and nitrogen isotopic composition (d13C, d15N) in marine sediments. Samples were collected during the Nansen Legacy cruises in March as part of cruise 2019711 (Q4) in the northern Barents Sea. Sediment material was subsampled from three replicate deployments of a giant box corer at three stations (P2 to P6). At P2, only two deployments were completed. All samples were freeze-dried under vacuum in the laboratory and homogenized. Elemental analysis of carbon and nitrogen concentrations was undertaken with an Elemental Analyser - Isotope Ratio Mass Spectrometry (EA-IRMS; Iso - Analytical Ltd., UK). Before d13C analysis, samples were acidified with 1M HCl and left overnight to allow the inorganic carbon to be liberated as CO2. The samples were then neutralized by repetitively washing with distilled water and oven drying at 60 degrees Celsius. The standards d13CV-PDB (Vienna PeeDee Belemnite) and d15NAIR (atmospheric N2) were used as references for the carbon and nitrogen isotope values, respectively. The measured TOC content was corrected for weight loss upon acid washing, TIC content was calculated by subtracting TOC from TC.
DOI: 10.25982/157793.280/2368552
title: KBase Narrative - 13 draft genomes of Bacillus from HLB-impacted citrus trees

description: We report the draft genome assembly, annotation and phylogenetic placement of 13 Bacillus spp. isolated from citrus groves under high (Florida) or low (California) Huanglongbing (HLB) disease pressure.
DOI: 10.3886/icpsr08185.v1
title: Calling the Police: Citizen Reporting of Serious Crime, 1979
title: Version 1

description: This dataset replicates the citizen reporting component of POLICE RESPONSE TIME ANALYSIS, 1975 (ICPSR 7760). Information is included on 4,095 reported incidents of aggravated assault, auto theft, burglary, larceny/theft offenses, forcible rape, and robbery. The data cover citizen calls to police between April 21 and December 7, 1979. There are four files in this collection, one each for Jacksonville, Florida, Peoria, Illinois, Rochester, New York, and San Diego, California. The data are taken from police dispatch records and police interviews of citizens who requested police assistance. Variables taken from the dispatch records include the dispatch time, call priority, police travel time, age, sex, and race of the caller, response code, number of suspects, and area of the city in which the call originated. Variables taken from the citizen interviews include respondent's role in the incident (victim, caller, victim-caller, witness-caller), incident location, relationship of caller to victim, number of victims, identification of suspect, and interaction with police.
description: Datasets: 
 
 DS0: Study-Level Files 
 DS1: Jacksonville, Florida 
 DS2: Peoria, Illinois 
 DS3: Rochester, New York 
 DS4: San Diego, California
DOI: 10.5066/f7h41pkx
title: County-Level Estimates of Nitrogen and Phosphorus from Commercial Fertilizer for the Conterminous United States, 1987-2012

description: This data set contains county-level estimates of nitrogen and phosphorus from fertilizer, for both farm and nonfarm uses, for the conterminous United States, for 1987 through 2012. State-level farm and nonfarm nitrogen and phosphorus were derived from the Association of American Plant Food Control Officials (AAPFCO) commercial fertilizer sales data. State estimates were then allocated to the county-level using fertilizer expenditure from the Census of Agriculture as county weights for farm fertilizer, and effective population density as county weights for nonfarm fertilizer. Data computations for 2007 - 2012 estimates are results of methods applied directly from Gronberg and Spahr, 2012. Data for 1987 - 2006 are exactly those published in Gronberg and Spahr, 2012. Gronberg, J.M., and Spahr, N.E., 2012, County-level estimates of nitrogen and phosphorus from commercial fertilizer for the Conterminous United States, 19872006: U.S. Geological Survey Scientific Investigations Report 2012-5207, 20 p. - https://pubs.usgs.gov/sir/2012/5207/
DOI: 10.58150/iea_timss_2019_g4
title: TIMSS 2019 International Database: Grade 4 - Trends in International Mathematics and Science Study

description: Trends in International Mathematics and Science Study 2019
TIMSS 2019 marks the seventh cycle of the study and provides 24 years of trends. Conducted every four years since 1995, TIMSS has been a valuable tool for monitoring international trends in mathematics and science achievement at the fourth and eighth grades.
TIMSS 2019 reported overall achievement, as well as extensive background information on the home and school contexts in which teaching and learning mathematics and science take place. Like the previous TIMSS assessments (conducted in 1995, 1999, 2003, 2007, 2011, and 2015), TIMSS 2019 collected detailed information about curriculum and curriculum implementation, instructional practices, and school resources.
From the 2019 cycle onwards, an innovative computerized version of TIMSS enables countries to investigate complex areas of the mathematics and science framework that are difficult to measure with traditional paper and pencil tests. eTIMSS is an engaging, interactive assessment that encompasses the content of the paper-and-pencil version of TIMSS while also integrating problem solving and inquiry tasks designed to stimulate student motivation through items that simulate real world contexts and laboratory situations. In 2019, countries could opt to administer the paper-based version of TIMSS. The next cycle of TIMSS will be administered in 2023.
description: TIMSS
description: Educational measurements and tests
description: <strong>Target population (students)</strong>
All students enrolled in the grades representing 4 years of formal schooling respectively, counting from the first year of ISCED Level 1.
description: STRATIFIED TWO-STAGE CLUSTER SAMPLE DESIGN
DOI: 10.6084/m9.figshare.23599461
title: Shotgun metagenome sequencing and recovery of 444 metagenome-assembled microbial genomes from the biofloc aquaculture system

description: We assembled a total of 444 medium- to high-quality metagenome-assembled genomes (MAGs) with completeness &gt; 50% and contamination &lt; 5%, from floc-associated bacterial community (FAB) of a commercial shrimp biofloc aquaculture system, located in South Korea.
DOI: 10.15472/ej32hn
title: Estudios bióticos (Plantas, Fauna Edáfica, Anfibios y Aves) en el Complejo de Páramos Perijá

description: Se incorporan los datos resultado del proyecto Delimitación de Páramo de la Serranía del Perijá. Donde se buscó conocer la composición y estructura de la vegetación y las comunidades de Edafofauna, Avifauna y Anfibios del complejo de páramos de la serranía del Perijá en los departamentos de la Guajira (municipio de la Jagua del Pilar) y el Cesar (municipios de Agustín Codazzi, Manaure y La Paz), en 4 transectos de un rango altitudinal de 1400 a 3400 m. La metodología empleada fue propuesta por el Instituto Alexander Von Humboldt por componente así: vegetación se muestreo por el método de parcelas; Avifauna con redes de niebla y punto de observación; Anfibios se trabajó con el método de búsqueda por encuentro casual (VES) y la Edafofauna con trampas de caída, jameo y colectas manuales. Los grupos taxonómicos encontrados para la vegetación fueron Magnoliophytas, Pteridophytas y Pinophytas con 2666 registros, en animales se registraron cordados de las clases anfibia con una sola especie y aves con 138 registros, así mismo en la edafofauna se registraron 6002 individuos mayormente de la clase insecta.
DOI: 10.24432/c53919
title: CDC Diabetes Health Indicators
DOI: 10.25828/47cd-z315
title: Township Smoking Study
DOI: 10.25828/d7z7-2k50
title: Gambia Tobacco Survey 2017
DOI: 10.25828/g2hk-ty68
title: Township Micro-enterprise Survey 2010-2013
DOI: 10.48612/msupe/d8r2-x43t-9h8h
title: Измерение наглядно-образного мышления дошкольников 5-6 лет по методике "Схематизация" (выборка стандартизации)

description: Представлены результаты измерения наглядно-образного мышления детей дошкольного возраста 5-6 лет (N = 974; из них 48,7% мужского пола; 51,3% женского пола) по методике "Схематизация 5-6 лет" (Бардина Р.И.), разработанной под руководством Л.А. Венгера и переведенной в цифровой вариант. В базе содержатся социально-демографические характеристики детей: пол ребёнка, возраст, тип образовательного учреждения, группа обучения, образовательная программа, регион проживания ребенка, тип поселения (городское, сельское), численность населения, указывались также некоторые особенности состояния здоровья ребенка (относится ли к категории детей с ОВЗ, имеет ли задержку психического развития, нарушение речи, слуха, зрения и т.д.). Для части детей (N = 41) из основной выборки приводятся измерения их интеллектуального развития с помощью методики "Цветные прогрессивные матрицы Равена". Сбор данных производился с помощью системы «Анкетолог». Данные использовались для стандартизации методики "Схематизация" для детей 5-6 лет.
DOI: 10.48612/msupe/zzg2-an91-h9nf
title: Измерение наглядно-образного мышления дошкольников 6-7 лет по методике "Схематизация" (выборка стандартизации)

description: Представлены результаты измерения наглядно-образного мышления детей дошкольного возраста 6-7 лет (N = 1451; из них 47,1% ребенка мужского пола; 52,9% женского пола) по методике "Схематизация 6-7 лет" (Бардина Р.И.), разработанной под руководством Л.А. Венгера и переведенной в цифровой вариант. В базе содержатся социально-демографические характеристики детей: пол ребёнка, возраст, тип образовательного учреждения, группа обучения, образовательная программа, регион проживания ребенка, тип поселения (городское, сельское), численность населения, указывались также некоторые особенности состояния здоровья ребенка (относится ли к категории детей с ОВЗ, имеет ли задержку психического развития, нарушение речи, слуха, зрения и т.д.). Для части детей (N = 527) из основной выборки приводятся измерения их интеллектуального развития с помощью методики "Цветные прогрессивные матрицы Равена". Сбор данных производился в цифровом формате с помощью системы «Анкетолог. Данные использовались для стандартизации методики "Схематизация" для детей 6-7 лет.
DOI: 10.5281/zenodo.10058762
title: Reproduction package for the paper "Two waves of massive stars running away from the young cluster R136"

description: Reproduction package for the paper "Two waves of massive stars running away from the young cluster R136".



This reproduction package aims for open science, with the internal API designation of 'Gold'

Authors: M. Stoop, A. de Koter, L. Kaper, S. Brands, S. Portegies Zwart, H. Sana, F. Stoppa, M. Gieles, L. Mahy, T. Shenar, D. Guo, G. Nelemans, S. Rieder

Paper DOI: https://doi.org/10.1038/s41586-024-08013-8

Zenodo DOI: http://doi.org/10.5281/zenodo.10058762

Published in Nature (date of publication: 2024/10/09)


Hardware



Tested on a MacBook Pro (13-inch, 2020, Four Thunderbolt 3 ports)

Processor: 2 GHz Quad-Core Intel Core i5

Memory: 32 GB 3733 MHz LPDDR4X

Graphics: Intel Iris Plus Graphics 1536 MB


Required non-standard hardware



None


Software dependencies



Jupyterlab (4.0.8)

Notebook (7.0.6)

Programming languages used: Python (3.11.7)

Python packages used: numpy (1.25.2), pandas (2.1.4), matplotlib (3.8.0), os (comes with Python) scipy (1.11.4), gaiadr3-zeropoint (0.0.4) https://gitlab.com/icc-ub/public/gaiadr3_zeropoint), astroquery (0.4.6), pymc (5.6.1), corner (2.2.2), arviz (0.16.0), pytensor (2.12.3), lmfit (1.2.2), powerlaw (1.5), rpy2 (3.5.16), seaborn (0.12.2), consistencytest (0.0.2)


Instructions



The Anaconda conda environment is given should this be needed

All Jupyter Notebooks are ready-made to produce the raw data, intermediate and end data products

Gaia raw data is downloaded in the Jupyter Notebook "R136_runaway_candidates.ipynb"

Data from the literature is given in the subdirectory /tables/ or /input_files/

Input images and files are given in the subdirectory /input_files/

Intermediate and end data products are given in /output_files/

Figures in the paper are produced in the Jupyter Notebooks in the subdirectory /figures/ and stored in the subdirectory /figures/figures_paper/


Expected Output



Jupyter Notebooks can be executed by "Run" -> "Run All Cells"

The Jupyter Notebook show the expected output in their respective cell

Expected runtime are given at the top of each Jupyter Notebook

The Jupyter Notebook which takes the longest "R136_runaway_search.ipynb" takes 7-8 hours for the entire dataset

A small dataset has been given in this Jupyter Notebook as a proof-of-concept


Instructions for use



Jupyter Notebooks can be executed by "Run" -> "Run All Cells"


Figures



Figures can be reproduced from the /figures/ folder.

All material and data used are available either in the Raw Data or in the Intermediate Data

The figures shown in the paper will be saved in ./figures/figures_paper/ folder.
DOI: 10.5281/zenodo.10700821
title: Annual crop-specific management history of phosphorus fertilizer input (CMH-P) in the croplands of United States from 1850 to 2022: Application rate, timing, and method

description: This dataset presents spatiotemporal dynamics of phosphorus (P) fertilizer management (application rate, timing, and method) at a 4km × 4 km resolution in agricultural land of the contiguous U.S. from 1850 to 2022. By harmonizing multiple data sources, we reconstructed the county-level crop-specific P fertilizer use history. We then spatialized and resampled P fertilizer use data to 4 km × 4 km gridded maps based on historical U.S. cropland distribution and crop type database developed by Ye et al. (2024).

This dataset contains (1) P fertilizer total consumption and mean application rate at the national level (Tabular); (2) P fertilizer consumption of 11 crops at the state level (Tabular); (3) P fertilizer consumption of permanent pasture (Tabular); (4) P fertilizer consumption of non-farm at the state level (Tabular); (5) P fertilizer application rate of 11 crop types at the state level (Tabular); (6) P fertilizer application rate of 11 crop types at the county level (Tabular); (7) P fertilizer application timing ratio at the state level (Tabular); (8) P fertilizer application method ratio at the state level (Tabular); (9) Gridded maps of P fertilizer application rate based on state-level data; (10) and (11) Gridded maps of P fertilizer application rate based on county-level data; (12)-(20) Gridded maps of P fertilizer application rate for each crop.

A detailed description of the data development processes, key findings, and uncertainties can be found in Cao, P., Yi, B., Bilotto, F., Gonzalez Fischer, C., Herrero, M., Lu, C.: Crop-specific Management History of Phosphorus fertilizer input (CMH-P) in the croplands of United States: Reconciliation of top-down and bottom-up data sources, is under review for the journal Earth System Science Data (ESSD). https://essd.copernicus.org/preprints/essd-2024-67/#discussion. 

This work is supported by the Iowa Nutrient Research Center, the ISU College of Liberal Arts and Sciences Dean's Faculty Fellowship, and NSF CAREER grant (1945036).
DOI: 10.5281/zenodo.13220167
title: Datasets underlying the paper 'Electrotaxis of self-propelling artificial swimmers in microchannels'

description: Datasets underlying the paper 'Electrotaxis of self-propelling artificial swimmers in microchannels', arXiv:2401.14376

Source data for all figures in the manuscript. Figures were produced by Python/matplotlib, a corresponding Jupyter notebook is included in the root folder. Compressed videomicrographs of the experiments, and abridged numerical data sets; all raw data are available from the authors on reasonable request.
DOI: 10.5281/zenodo.13364410
title: A Case Study of Thermospheric Exospheric Temperature Responses during the G-condition at Mohe and Beijing Stations

description: The Data presents the data shown in Figure 1-3.Geomagnetic_condition.mat includes the data of IMF By, IMF Bz, Dst index, Kp index and F107 index presented in Figure 1.observations.mat includes the data of peak Ne and Peak Ne height at Mohe and Beijing presented in Figure 2a and 2b.Retrieved_Tex.mat includes the data of retrieved Tex at Mohe and Beijing presented in Figure 2c and 2d.Chemiccal_reaction_rate_and_O_to_N2.mat includes the data of chemical reaction rate and O/N2 at Mohe and Beijing presented in Figure 3.ionogram.rar includes ionograms at Beijing and Mohe during the G-condition. Title of each ionogram is named as 'XXXXUT(XXXXLT)', representing hour and second in universal time and in local time.For instance, '0015UT(0800LT)' corresponds to 00:15 UT and 8:00 LT.
DOI: 10.5281/zenodo.13472805
title: Wave-influenced Delta Morphodynamics, Long-term Sediment Bypass and Trapping Controlled by Relative Magnitudes of Riverine and Wave-driven Sediment Transport

description: This repository contains supporting data for *Wave-influenced Delta Morphodynamics, Long-term Sediment Bypass and Trapping Controlled by Relative Magnitudes of Riverine and Wave-driven Sediment Transport,* submitted to Geophysical Research Letters.

Delft3D Config for Q1000Qs100Hs15.docx → contains configuration file info for running the Delft3d simulation Q1000Qs100Hs15.

Matlab 2022b was used to load Delft3D output files and process the data.

WaveDelta_Depth&DepositThick.mat Contains:

Depth → timesteps x 322 x 142. Timesteps are variable for each simulation.

MSEDRiverSum → 4 x 322 x 142. Mass of sediments from riverine source at four intermediate timesteps. 

MSEDWaveSum → 4 x 322 x 142. Mass of sediments from longshore transport (LSTUp) source at four intermediate timesteps.

VolRiverSum → 322 x 142. Final Volume of sediments from riverine source.

VolWaveSum → 322 x 142. Final Volume of sediments from longshore transport (LSTUp) source.

XCOR & YCOR are the X and Y grid coordinate locations for maps (322 x 142).

Shift2&4km are used for cases highly skewed downdrift to correct for 0 location at the river mouth.

Cerc_formula.mlx Computes CERC longshore transport for the simulation conditions.

J.mlx calculates river mouth balance (J) values (Nienhuis et al. (2016)) presented in Figure S4. 

Additional 114 Figures are provided in Data_Visualization_Figures.rar to show Depth and thickness; subaqueous morphodynamics and depth and sediment transport (quiver).
DOI: 10.5281/zenodo.3967291
title: SpaGE Spatial Gene Enhancement using scRNA-seq

description: Spatial transcriptomics and scRNA-seq datasets using for integration and prediction of spatially non-measured genes using SpaGE