cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20277606
title: Cellular Lifespan Seahorse Bioenergetics Raw Data

description: The current dataset provides Seahorse bioenergetic measures across the entire replicative lifespan of primary human fibroblast cell lines from n=6 healthy male and female donors and n=3 donors with lifespan-altering mitochondrial disease caused by mutations in the SURF1 gene. These datasets can be integrated with other omic measures collected in parallel along the cellular lifespan, including gene expression (RNA sequencing) and DNA methylation (GSE179849).This dataset also includes experimental manipulations with treatments targeting oxidative phosphorylation (OXPHOS) and glycolysis, and glucocorticoid signaling, providing an opportunity to examine the influence of stress and bioenergetics on human aging biology. All processed data can be accessed and browsed at our webtool: https://columbia-picard.shinyapps.io/shinyapp-Lifespan_Study/. A detailed description of the study and associated methods can be found at: https://www.biorxiv.org/content/10.1101/2021.11.12.468448
DOI: 10.6084/m9.figshare.4434800
title: Genes present in the core resistome of E. coli

description: This table lists genes we identified as present in at least 95 % of the <i>E. coli</i> genome sequences. The resistance profiles for each gene are listed.
DOI: 10.5066/p9x513wo
title: Simulated groundwater residence times in two principal aquifers of the Mississippi embayment physiographic region

description: Groundwater residence times and flow path lengths were simulated for two major aquifers of the Mississippi embayment region using particle tracking (Pollock, 2012; Starn and Belitz, 2018) in a regional groundwater-flow model (Haugh and others, 2020). The Mississippi embayment physiographic region includes two principal aquifer systems: the surficial aquifer system, which is dominated by the Quaternary Mississippi River Valley alluvial aquifer (MRVA), and the Mississippi embayment aquifer system, which includes deeper Tertiary aquifers and confining units. The groundwater residence time simulation focused on the MRVA and two hydrogeologic units of the Claiborne Group (CLBG) from the deeper system, including the middle Claiborne aquifer (MCAQ) and lower Claiborne aquifer (LCAQ). A previously published groundwater flow model of the Mississippi embayment regional aquifer system provided the flow field for this analysis (Clark and Hart, 2009; Clark and others, 2011; and Haugh and others, 2020). Raster files were produced for seven model layers following the hydrogeologic framework for the MODFLOW groundwater-flow model of the Mississippi embayment from Clark and Hart (2009): one for the MRVA and six for the middle and lower Claiborne aquifers including four representing the MCAQ (layers 5 - 8) and two representing the LCAQ (layers 9 and 10). To determine the groundwater residence time, particles were distributed in model layers representing these aquifers using a volume-weighted algorithm then back-tracked until the particles exited the aquifer system, usually at the water-table surface. Particles were tracked under transient hydrologic conditions from March 31, 2014 backwards to January 1, 1870, then under steady-state conditions until they exited the aquifer system. The simulated residence time of each particle is the time the particle took to travel backwards from its initial location in the aquifer to its source of origin. Groundwater-residence time metrics were generated by statistically summarizing individual particles that started within each model cell. The flow-model grid resolution of one square mile was used to simulate groundwater residence times. The data were then resampled to a 1-square kilometer resolution of the National Hydrologic Grid (Clark and others, 2018). Computed metrics included the minimum, mean, maximum, standard deviation, as well as the 10th-, 20th-, 30th-, 40th-, 50th-, 60th-,70th-, 80th-, and 90th-percentiles along with the minimum, median, and maximum flow path length. Additionally, the portion of young groundwater (&amp;lt; 65 years old) and the mean residence time of the young portion were computed.
DOI: 10.5281/zenodo.6405564
title: A global land surface 250-m 8-day Fraction of Absorbed Photosynthetically Active Radiation (FAPAR) product (2022-part1)

description: The Fraction of Absorbed Photosynthetically Active Radiation (FAPAR) is a critical land surface variable for carbon cycle modeling and ecological monitoring. We generated the latest version (V6) of the FAPAR product at a 250-m resolution, which is also aggregated to multiple coarser resolutions (up to 0.25° and monthly), from MODIS surface reflectance data and other information, as part of the Global Land Surface Satellite (GLASS) products suite. Three existing global FAPAR products (MODIS Collection 6, GLASS V5, and PROBA-V V1) were used to generate the time-series training samples for developing the Bidirectional Long Short-Term Memory (Bi-LSTM) model. Direct validation using high-resolution FAPAR maps from VALERI and ImagineS networks revealed that the GLASS V6 FAPAR product achieves higher accuracy than PROBA-V, MODIS, and GLASS V5, with R<sup>2</sup> of 0.80 and RMSE of 0.10-0.11 at the 250-m, 500-m, and 3-km scales, and a higher percentage (72%) of retrievals in meeting accuracy requirement of 0.1. Global spatial evaluation and temporal comparison at the Ameriflux and NEON sites indicated that the GLASS V6 FAPAR is more spatio-temporal continuous and better reflects the variations of vegetation than the GLASS V5 FAPAR. The temporal span of GLASS V6 FAPAR product is from 2000 to 2020 and the temporal frequency is 8-day. The 250-m and 500-m data are in the Sinusoidal projection, while the 0.05°, 0.1° and 0.25° data are in geographic latitude/longitude. Data files are provided in HDF−EOS format.
description: Due to the upload size restrictions, only the dataset for 2020 is included on this site, The 250-m GLASS V6 FAPAR product is freely available at www.glass.umd.edu. We have also aggregated it to coarser resolutions (500-m/8-day, 0.05°/8-day, 0.1°/month, 0.25°/month).
DOI: 10.6084/m9.figshare.12084669.v1
title: TCGA Pan-Cancer TIMER-based immune cell infiltration abundances

description: TCGA pan-cancer TIMER (Tumor IMmune Estimation Resours)-based immune cell infiltration abundances, including B cell, CD4+ T cell, CD8+ T cell, Dendritic, Macrophage and Neutrophil.
DOI: 10.6084/m9.figshare.12084693.v1
title: GPR18 mRNA expression levels in immune cell lines

description: The <i>GPR18</i> expression data in immune cell lines was got from the Human Primary Cell Atlas (HPCA). The immune cell lines include B cell, CD4+ T cell, CD8+ T cell, Macrophage, Neutrophil and Dendritic.
DOI: 10.6084/m9.figshare.19713841
title: Supplementary Material for: Innate Immune Responses to RSV Infection Facilitated by OGG1, an Enzyme Repairing Oxidatively Modified DNA Base Lesions

description: The primary cause of morbidity and mortality from infection with respiratory syncytial virus (RSV) is the excessive innate immune response(s) (IIR) in which reactive oxygen species (ROS) play key role(s). However, the mechanisms for these processes are not fully understood. We hypothesized that expressions of IIR genes are controlled by the ROS-generated epigenetic-like mark 7,8-dihydro-8-oxo(d)guanine (8-oxo(d)Gua) and 8-oxoguanine DNA glycosylase1 (OGG1). Here, we report that ROS not only generates intrahelical 8-oxo(d)Gua, but also enzymatically disables OGG1 in RSV-infected human airway epithelial cells and mouse lungs. OGG1 bound to 8-oxo(d)Gua in gene regulatory sequences promotes expression of IIR genes, and consequently exacerbates lung inflammation, histological changes, and body weight loss of experimental animals. Pharmacological inhibition of OGG1 substrate binding decreased expression of RSV-induced chemokine and cytokines and significantly lessened clinical symptoms. Results of mechanistic studies show that OGG1 binding at 8-oxo(d)Gua promoter regions modulated loading of transcription factors via transient cooperative interactions in RSV-infected lungs and airway epithelial cells. Other base specific DNA repair proteins had no effects. Collectively, this study identifies unprecedented roles of ROS-generated DNA base lesion(s) and cognate repair protein as a determinant of RSV-induced exuberant inflammation. Pharmaceutical inhibition of OGG1 interaction with its DNA substrate may represent a novel strategy in prevention/intervention of respiratory viral infections.
DOI: 10.34740/kaggle/dsv/4044806
title: Building and Vegetation Height Model of São Paulo
DOI: 10.3886/icpsr08236.v1
title: Census of Population, 1940 [United States]: Public Use Microdata Sample
title: Version 1

description: The 1940 Census Public Use Microdata Sample Project was assembled through a collaborative effort between the United States Bureau of the Census and the Center for Demography and Ecology at the University of Wisconsin. The collection contains a stratified 1-percent sample of households, with separate records for each household, for each "sample line" respondent, and for each person in the household. These records were encoded from microfilm copies of original handwritten enumeration schedules from the 1940 Census of Population. Geographic identification of the location of the sampled households includes Census regions and divisions, states (except Alaska and Hawaii), standard metropolitan areas (SMAs), and state economic areas (SEAs). Accompanying the data collection is a codebook that includes an abstract, descriptions of sample design, processing procedures and file structure, a data dictionary (record layout), category code lists, and a glossary. Also included is a procedural history of the 1940 Census. Each of the 20 subsamples contains three record types: household, sample line, and person. Household variables describe the location and condition of the household. The sample line records contain variables describing demographic characteristics such as nativity, marital status, number of children, veteran status, wage deductions for Social Security, and occupation. Person records also contain variables describing demographic characteristics including nativity, marital status, family membership, education, employment status, income, and occupation.
description: The 1940 Census had both a complete count and a sample component. Individuals selected for the sample component were asked an additional set of questions. Only households with persons who answered the additional questions were included in the public use microdata sample. The collection also contains records of group quarters members who were also on the Census sample line. The 20 subsamples were selected randomly.
description: Datasets: DS0: Study-Level Files DS1: Subsample 1 DS2: Subsample 2 DS3: Subsample 3 DS4: Subsample 4 DS5: Subsample 5 DS6: Subsample 6 DS7: Subsample 7 DS8: Subsample 8 DS9: Subsample 9 DS10: Subsample 10 DS11: Subsample 11 DS12: Subsample 12 DS13: Subsample 13 DS14: Subsample 14 DS15: Subsample 15 DS16: Subsample 16 DS17: Subsample 17 DS18: Subsample 18 DS19: Subsample 19 DS20: Subsample 20
description: All people and households within the United States recorded on the 1940 Census.
description: The data files are arranged by subsample, with each subsample stored as a separate physical file of information. Within each of the 20 subsamples, records are sequenced by state. Extracting all of the records for one state entails reading through all of the 20 physical files and selecting that state's records from each of the 20 subsamples.The collection consists of a total of 2,133,800 hierarchical records: 391,034 household records, 391,034 sample line records, and 1,351,732 person records.
DOI: 10.5281/zenodo.4599735
title: Tracking Selection using Temporal Population Genomics Data

description: This repository contains the implementation of a pipeline to run the simulations and to produce a reference table for the ABC-RF inference of demography and selection. In its new release, this repository contains the whole-genome polymorphism of contemporary and museum specimens of <em>Apis mellifera</em> feral populations analyzed by Cridland et al. (2018).
DOI: 10.5281/zenodo.6336118
title: In vitro vs. In planta: Akanthomyces lecanii compatibility Dataset

description: In vitro and in planta raw data
DOI: 10.5281/zenodo.7271441
title: Morphological measurements of coccoliths from surface samples of South China Sea

description: The dataset compiles morphological measurements of coccoliths (<em>Gephyrocapsa</em> spp. and <em>Emiliania huxleyi</em>, &gt;2µm) from surface samples of the South China Sea retrieved at different depths of the basin during the R/V Sonne cruises (SO-95); and of Gephyrocapsa spp. from one sample from the Western Equatorial Pacific (ODP 807A, -2H-2W, 57-59 cm) used in a dissolution experiment. The columns include station names, Longitude, Latitude, Depth (m), how much Calgon was added into sediment suspension (in the dissolution experiment), number of coccoliths measured per sample, mean ks shape factor, thickness, length, volume, mass, and standard deviation of mean ks/mean ks.
description: Grants: Coordenação de Aperfeiçoamento de Pessoal de Nível Superior – Brazil (CAPES) - Finance Code 001; CAPES-PRINT – Programa Institucional de Internacionalização - Process: 88887.571907/2020-00; National Natural Science Foundation of China (grants 42188102 and 41930536 to C.L).
DOI: 10.17632/9x9vjwd7ry.1
title: Germination of grass caryopses at increasing water deficit under simulated current and future temperature regimes

description: Our proposal was to study the impacts of increasing water stress and temperature on the survival and germination of caryopses of neotropical grass species occurring in dry- and wet grasslands of the Cerrado biome (Brazil). The Cerrado is the second largest biome of the South America, largely covered by savanna and other vegetation types subjected to periodic fires, as the grasslands. Considering that dry grasslands are subjected to higher soil temperatures and water deficit than wet grasslands, our expectation was that caryopses from dry grassland species would be more tolerant to both increasing water stress and higher temperatures (predicted for the future) than caryopses from wet grassland species. We found that more intense water stress reduced the survival of caryopses for both dry and wet grassland species. Temperature regime predicted for the future reduced the viability of wet grassland species and affected the germination strategy of dry grassland species. These results indicate that increasing water stress and temperature predicted for the future may compromise the recruitment potential of dry and wet grassland species, thus directly impacting the dynamics and resilience of these ecosystems in a future scenario. 
This study was recently accepted for publication at the American Journal of Botany (2022). The table here provided brings data on the germinability (%), median germination time (T50, in hours) and viability (%) of neotropical grass caryopses from dry and wet grasslands subjected to increasing water stress treatments under simulated current and future temperature regimes. We have organized the data to facilitate its analysis in R. It is quite self-explanatory, but one can find a tab (metadata) which details each variable. The R script used in the present study is also provided.
DOI: 10.18739/a28g8fj7f
title: Modèle Atmosphérique Régional (MAR) version 3.11 regional climate model output, 1979-2019, Greenland domain, 10 kilometer (km) horizontal resolution

description: Modèle Atmosphérique Régional (MAR) is a regional climate model that is fully coupled to a one-dimensional surface-atmosphere energy and mass transfer scheme, SISVAT (Soil Ice Snow Vegetation Atmosphere Transfer) (Fettweis et al., 2005, 2020; Lefebre et al., 2005). SISVAT employs a multilayered snowpack model, CROCUS, that simulates meltwater production, percolation, and refreeze (Brun et al., 1989), while also accounting for changes in albedo due to snow metamorphism (Brun et al., 1992). MAR has been extensively verified over the Greenland Ice Sheet and is therefore particularly well suited for analyses of Greenland ice sheet surface mass balance (Fettweis et al., 2011; Fettweis et al., 2020; Lefebre et al. 2005; Mattingly et al. 2020). Brun, E., Martin, E., Simon, V., Gendre, C., and Coléou, C. (1989). An energy and mass model of snow cover suitable for operational avalanche forecasting. Journal of Glaciology, 35, 333. https://doi.org/10.1017/S0022143000009254 Brun, E., David, P., Sudul, M., and Brunot, G. (1992). A numerical model to simulate snow-cover stratigraphy for operational avalanche forecasting. Journal of Glaciology, 38(128), 13–22. https://doi.org/10.3189/S0022143000009552 Fettweis, X., Gallée, H., Lefebre, F., and van Ypersele, J.-P. (2005). Greenland surface mass balance simulated by a regional climate model and comparison with satellite-derived data in 1990–1991. Climate Dynamics, 24(6), 623–640. https://doi.org/10.1007/s00382-005-0010-y Fettweis, X., Tedesco, M., van den Broeke, M., and Ettema, J. (2011). Melting trends over the Greenland ice sheet (1958–2009) from spaceborne microwave data and regional climate models. The Cryosphere, 5(2), 359–375. https://doi.org/10.5194/tc-5-359-2011 Fettweis, X., Hofer, S., Krebs-Kanzow, U., Amory, C., Aoki, T., Berends, C. J., et al. (2020). GrSMBMIP: intercomparison of the modelled 1980–2012 surface mass balance over the Greenland Ice Sheet. The Cryosphere, 14(11), 3935–3958. https://doi.org/10.5194/tc-14-3935-2020 Lefebre, F., Fettweis, X., Gallée, H., Van Ypersele, J.-P., Marbaix, P., Greuell, W., and Calanca, P. (2005). Evaluation of a high-resolution regional climate simulation over Greenland. Climate Dynamics, 25(1), 99–116. https://doi.org/10.1007/s00382-005-0005-8 Mattingly, K. S., Mote, T. L., Fettweis, X., van As, D., Van Tricht, K., Lhermitte, S., et al. (2020). Strong summer atmospheric rivers trigger Greenland ice sheet melt through spatially varying surface energy balance and cloud regimes. Journal of Climate, 33(16), 6809–6832. https://doi.org/10.1175/JCLI-D-19-0835.1
DOI: 10.18739/a2zs2kd0z
title: Surface Mass Balance and Snow Depth on Sea Ice Working Group (SUMup) accumulation on land ice subdataset, Greenland and Antarctica, 1987-2018

description: This dataset includes accumulation on land ice measurements from both hemispheres. This dataset is a community effort to distribute easy to use in-situ data to improve surface mass balance modeling and remote sensing efforts. This dataset is a compilation of work from many individual researchers. When using this dataset please cite both the individual researchers who provided the data as listed in the Citation field as well as this dataset. The snow accumulation on land ice subdataset contains over 300,000 data points. The Arctic accumulation measurements, all within Greenland, contain 48% of the measurements with ~1% coming from Summit Station. The Antarctic contains the remaining 51% of the measurements. While most of the data are measurements of accumulation between 1950 and present (~97%), to coincide with the time span of many regional climate models and reanalysis products, some records (~3%) are included dating back to 1800. The measurement methods include ice cores, snow pits, radar isochrons, and stake measurements. Fields of data include the date taken, latitude, longitude, start year and end year (if not an annual measurement), year (if annual), accumulation, error, elevation, radar horizontal resolution, method, name of field campaign, and associated citation.
DOI: 10.3886/e144904v2
title: Census Tree Links

description: The data sets in this repository allow users to link people among the U.S. decennial censuses, using the "histid" identifier. The census data sets users will need are indexed by Ancestry.com and are hosted by IPUMS at https://usa.ipums.org/usa-action/samples. Users will need to download the full-count census for each year and be sure to select the "histid" variable that is available under the Person/Historical Technical drop-down menu.<br><br>As of 7/12/21, links are available between the 1900-1910, 1910-1920, and 1900-1920 censuses.<br><br>A detailed account of how these links are created and a description of the data and its characteristics are available in the following article:<br><br><b>Price, J., Buckles, K., Van Leeuwen, J., & Riley, I. (2021). Combining family history and machine learning to link historical records: The Census Tree data set. </b><b>Explorations in Economic History</b><b>, </b><b>80</b><b>, 101391.</b><br>https://www.sciencedirect.com/science/article/pii/S0014498321000024<br>
DOI: 10.5066/f7n878qn
title: Digitized Plates of "Geomorphology and Quaternary Geologic History of the Lower Mississippi Valley," From Saucier (1994)
DOI: 10.5281/zenodo.4000171
title: DATA & CODE for "Substrate-dependent fish have shifted less in distribution under climate change"

description: Authors: Sarah M. Roberts*<sup>1</sup>, Andre M. Boustany<sup>2</sup>, Patrick N. Halpin<sup>1</sup> <strong>Author affiliations: </strong> *<sup>1</sup>Marine Geospatial Ecology Lab, Nicholas School of the Environment and Earth Sciences, Duke University, Durham, NC 27708, US <sup>2 </sup>Monterey Bay Aquarium, 886 Cannery Row, Monterey, CA 93940, USA This dataset and code run the necessary methods for the manuscript titled: "<strong>Substrate-dependent fish have shifted less in distribution under climate change. </strong><strong>Substrate-dependent fish have shifted less in distribution under climate change" </strong>published in Nature Communications Biology. In order to run the code, you need to request data from https://oceanadapt.rutgers.edu/. The download is free, I just don't have permission to publish their data. Software needed is Rstudio and R.
DOI: 10.5281/zenodo.4069473
title: Supplemental information for McClelland et al. (2020). Management of cover crops in temperate climates influences soil organic carbon stocks – A meta-analysis

description: All supplemental information for McClelland et al. (2020). Management of cover crops in temperate climates influences soil organic carbon stocks – A meta-analysis.
DOI: 10.5281/zenodo.6430925
title: A global land surface 250-m 8-day Fraction of Absorbed Photosynthetically Active Radiation (FAPAR) product (2022-part2)

description: The Fraction of Absorbed Photosynthetically Active Radiation (FAPAR) is a critical land surface variable for carbon cycle modeling and ecological monitoring. We generated the latest version (V6) of the FAPAR product at a 250-m resolution, which is also aggregated to multiple coarser resolutions (up to 0.25° and monthly), from MODIS surface reflectance data and other information, as part of the Global Land Surface Satellite (GLASS) products suite. Three existing global FAPAR products (MODIS Collection 6, GLASS V5, and PROBA-V V1) were used to generate the time-series training samples for developing the Bidirectional Long Short-Term Memory (Bi-LSTM) model. Direct validation using high-resolution FAPAR maps from VALERI and ImagineS networks revealed that the GLASS V6 FAPAR product achieves higher accuracy than PROBA-V, MODIS, and GLASS V5, with R<sup>2</sup> of 0.80 and RMSE of 0.10-0.11 at the 250-m, 500-m, and 3-km scales, and a higher percentage (72%) of retrievals in meeting accuracy requirement of 0.1. Global spatial evaluation and temporal comparison at the Ameriflux and NEON sites indicated that the GLASS V6 FAPAR is more spatio-temporal continuous and better reflects the variations of vegetation than the GLASS V5 FAPAR. The temporal span of GLASS V6 FAPAR product is from 2000 to 2020 and the temporal frequency is 8-day. The 250-m and 500-m data are in the Sinusoidal projection, while the 0.05°, 0.1° and 0.25° data are in geographic latitude/longitude. Data files are provided in HDF−EOS format.
description: Due to the upload size restrictions, only the dataset for 2020 is included on this site, The 250-m GLASS V6 FAPAR product is freely available at www.glass.umd.edu. We have also aggregated it to coarser resolutions (500-m/8-day, 0.05°/8-day, 0.1°/month, 0.25°/month).