cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5066/f7xp732p
title: Data for evaluating the Sr/Ca temperature proxy with in-situ temperature in the western Atlantic coral Siderastrea siderea

description: Massive corals are used as environmental recorders throughout the tropics and subtropics to study environmental variability during time periods preceding ocean-observing instrumentation. However, careful testing of paleoproxies is necessary to validate the environmental-proxy record throughout a range of conditions experienced by the recording organisms. As part of the USGS Coral Reef Ecosystems Studies project, we tested the hypothesis that the coral Siderastrea siderea faithfully records sea-surface temperature (SST) in the Sr/Ca record throughout the subtropical (Florida, USA) seasonal cycle along 350 km of reef tract. Coral samples were analyzed from thirty-nine corals growing in 3 to 4 m depth at Fowey Rocks (Biscayne National Park), Molasses Reef (Florida Keys National Marine Sanctuary, FKNMS), Sombrero Reef (FKNMS), and Pulaski Shoal (Dry Tortugas National Park). Temperatures were recorded with Onset HOBO Water Temp Pro V2 (U22-001) data loggers in duplicate at each site. Sr/Ca, Mg/Ca, calcification rate, and select underwater temperature data are provided here. The results of this experiment are interpreted in Kuffner and others (2017). A larger temperature dataset, including the data provided here, is found in another data release Kuffner (2016), and a larger calcification-rate dataset is interpreted in Kuffner and others (2013). Kuffner, I. B., Roberts, K.E., Flannery, J.A., Morrison, J.M., and Richey, J.N., 2017, Fidelity of the Sr/Ca proxy in recording ocean temperature in the western Atlantic coral Siderastrea siderea: Geochemistry, Geophysics, Geosystems, v. 18, no. 1, p. 178-188, https://doi.org/10.1002/2016GC006640. Kuffner, I.B., T.D. Hickey, and J.M. Morrison, 2013, Calcification rates of the massive coral Siderastrea siderea and crustose coralline algae along the Florida Keys (USA) outer-reef tract: Coral Reefs, v. 32, p. 987-997, https://doi.org/10.1007/s00338-013-1047-8. Kuffner, I.B., 2016, Underwater temperature on off-shore coral reefs of the Florida Keys, U.S.A. (ver. 6.0, February 2021): U.S. Geological Survey data release, https://doi.org/10.5066/F71C1TZK.
DOI: 10.5281/zenodo.8228690
title: Supplementary files for John et al. 2023

description: Intended for those reading John et al. 2023 Contains: Supplementary Information file (.pdf) to accompany main text. Includes more detailed methodology, as well as additional figures. EPMA maps (.tif) of Eocene <em>M. aragonensis </em>and <em>M. crater</em> plus matlab scripts for generating figures.
DOI: 10.5439/1039926
title: ARM Climate Modeling Best Estimate Lamont, OK (ARMBE-CLDRAD SGPC1)

description: The ARM CMBE-ATM [Xie, McCoy, Klein et al.] data file contains a best estimate of several selected atmospheric quantities from ACRF observations and NWP analysis data.
DOI: 10.6073/pasta/58414574e57fd558d71cfab0952c0dc1
title: Common snook (Centropomus undecimalis) movements within the Shark River estuary (FCE), Everglades National Park, South Florida from February 2012 to Present
DOI: 10.6084/m9.figshare.956138
title: Gaussian Job Archive for C12H11ClN2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.956213
title: Gaussian Job Archive for C12H11ClN2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.15784/601540
title: Siple Dome Surface Energy Flux

description: This data set comprises radiative and turbulent flux components of the surface energy balance at Siple Dome, West Antarctica, measured between 21 December 2019 and 19 January 2020. Radiative fluxes were measured by Kipp & Zonen pyranometers and pyrgeometers. A Campbell Scientific open path eddy covariance system measured sensible and latent heat fluxes. An Apogee infrared sensor measured surface skin temperature. Sky conditions were observed using an ALCOR System digital all-sky camera. A StellarNet shortwave spectroradiometer system measured downwelling spectral irradiance in the wavelength range 350-1700 nm.
DOI: 10.5066/f7222t0m
title: Qualitative and quantitative surveys of native freshwater mussels in the upper and middle Delaware River (2000-2002)

description: Data is included for two types of field surveys conducted for freshwater mussels in the mainstem of the middle and upper Delaware River in the Mid-Atlantic region of the United States from 2000-2002. Timed search (qualitative) surveys were conducted during 2000-2001 from a point at the confluence of the East and West Branches of the Delaware River near Hancock, NY continuously downstream to a point at the mouth of the Paulins Kill River near Columbia, NJ. In this qualitative survey, mussel species and counts were collected in the field catch-per-unit-effort (CPUE) data was determined for all mussel species within each of 1,095 consecutive stream sections ~200 m in length. Subsequent quantitative surveys were conducted in select 200-m sections of river using quadrats during 2002 in order to estimate abundance and density of mussel present in these sections. One Excel file contains data from qualitative surveys, and a second excel file contains data from quantitative quadrat surveys.
DOI: 10.5281/zenodo.1045871
title: Nahal Haarava Data And Models V1.0.1

description: Data and models for Nahal HaArava project
DOI: 10.6073/pasta/695377795987881f8877280a20cd9c9e
title: Forest Inventory of a Northern Hardwood Forest:
    Watershed 6 1982, Hubbard Brook Experimental Forest

description: Forest inventory surveys were initiated in 1965,
      repeated in 1977, and repeated at 5 year intervals after
      that; this data set was collected in summer of 1982. The
      inventory consists of a total inventory of all trees &gt;=10
      cm diameter-at-breast-height (dbh) on the whole of the
      watershed (13.23 ha), as measured in each of the 208 25 m x
      25 m plots. Trees &gt;=2 to &lt;=10 cm dbh were inventoried
      on 35 of the 25 m x 25 m plot.
      These data were gathered as part of the Hubbard Brook
      Ecosystem Study (HBES). The HBES is a collaborative effort at
      the Hubbard Brook Experimental Forest, which is operated and
      maintained by the USDA Forest Service, Northern Research
      Station.
DOI: 10.6073/pasta/a58f3929f45b56357b23d60db85b09f3
title: Forest Inventory of a Northern Hardwood Forest:
    Watershed 6 1977, Hubbard Brook Experimental Forest

description: Forest inventory surveys were initiated in 1965,
      repeated in 1977, and repeated at 5 year intervals after
      that; this data set was collected in summer of 1977. The
      inventory consists of a total inventory of all trees &gt;=10
      cm diameter-at-breast-height (dbh) on the whole of the
      watershed (13.23 ha), as measured in each of the 208 25 m x
      25 m plots. Trees &gt;=2 to &lt;=10 cm dbh were not measured
      in 1977.
      These data were gathered as part of the Hubbard Brook
      Ecosystem Study (HBES). The HBES is a collaborative effort at
      the Hubbard Brook Experimental Forest, which is operated and
      maintained by the USDA Forest Service, Northern Research
      Station.
DOI: 10.6073/pasta/cb27c135b9f6f894507f24761b25a3e2
title: Forest Inventory of a Northern Hardwood Forest:
    Watershed 6 1965, Hubbard Brook Experimental Forest

description: Forest inventory surveys were initiated in 1965,
      repeated in 1977, and repeated at 5 year intervals after
      that. This is the initial data set and was collected in
      summer of 1965. The inventory consists of a total inventory
      of all trees &gt;= 1.5 cm diameter-at-breast-height (dbh) on
      the whole of the watershed (13.23 ha), as measured in each of
      the 208 25 m x 25 m plots. Shrubs, seedlings and small
      saplings were also surveyed.
      These data were gathered as part of the Hubbard Brook
      Ecosystem Study (HBES). The HBES is a collaborative effort at
      the Hubbard Brook Experimental Forest, which is operated and
      maintained by the USDA Forest Service, Northern Research
      Station.
DOI: 10.6073/pasta/fb658789188724be5f27c81a634647d5
title: Zooplankton collected with a 2-m, 700-um net towed from surface to 120 m, aboard Palmer Station Antarctica LTER annual cruises off the western antarctic peninsula, 2009 - 2016.
DOI: 10.6084/m9.figshare.811862
title: Script for creating an NCI surface as a JVXL compressed file from a (Gaussian) cube of total electron density

description: A Script to generate a NCI surface from a Gaussian Cube file, and to write the result as two files, a .xyz coordinate file and a .jvxl isosurface file. See E. R. Johnson, S. Keinan, P. Mori-Sánchez, J. Contreras-García, A. J. Cohen and W. Yang, J. Am. Chem. Soc., 2010, 132, 6498–6506. doi: 10.1021/ja100936w for details of the theoretical procedure. The NCI procedure was implemented in Jmol by Bob Hanson.
DOI: 10.6073/pasta/37ff12d47894a73ddd9d86c1225e2dc8
title: Biomass Inventories at Harvard Forest EMS Tower since 1993

description: In 1993, we installed 40 circular, 10 m radius biometric plots in the footprint of the EMS tower on Prospect Hill. We randomly placed the plots within 100 m increments along ten 500 m transects that extend from the tower in the northwest and southwest directions. In 2001, we removed three plots (G3, H3, H4) from the datasets and ceased measurements there due to their inundation by a beaver pond. In 1999, we installed 6 additional circular, 10 m radius biometric plots on the Simes Lot, adjacent to Prospect Hill to study the effects of a selective harvest that occurred there in the winter of 2000-01. In the summer of 2001, we expanded the harvested plots in size to 15 m radius and ceased measurements at one plot (X4) because it was unaffected by the harvest. The harvest also affected three of the original tower plots (A4, A5, B5), which were expanded in size as a part of the harvest plot group. Consequently, there are 34 tower plots and 8 harvest plots. We have taken the following ecological measurements at each site: tree growth, woody debris, litter, leaf area increment (LAI), leaf chemistry, and soil respiration and moisture.
DOI: 10.6084/m9.figshare.24146292
title: Supplementary Material for: Two distinct characteristics of immune microenvironment in human hepatocellular carcinoma with Wnt/β-catenin mutations

description: Introduction Immunotherapy is becoming a promising approach for unresectable-hepatocellular carcinoma (HCC); the anti-tumor response is affected by the tumor microenvironment (TME). Although Wnt/β-catenin mutations are reported to cause non-inflamed phenotype, their role on TME remains controversial. We aimed to clarify the heterogeneity of immunophenotype in HCC with Wnt/β-catenin mutations. Methods This study includes 152 resected HCCs; mutations in the catenin beta-1, adenomatous polyposis coli, or AXIN1, or AXIN2 genes were defined as Wnt/β-catenin mutations. With hierarchical cluster analyses, TME were classified into inflamed or non-inflamed classes based on the gene expressions associated with T-cell activation. Expression profiles of molecules related to cell differentiation and biliary-stem cell markers were compared between the TME classes to investigate whether differences in tumor traits were associated with TME. Results Forty of 152 (26.3%) HCCs carried the Wnt/β-catenin mutations. Of these, 33 were classified as non-inflamed (33/40, 82.5%) and 7 as inflamed (7/40, 17.5%). Non-inflamed class was characterized by low number of CD3+, CD4+, and CD8+ cells on immunostaining, and high mRNA expressions of AXIN2 and GLUL, which are involved in the canonical Wnt/β-catenin signaling and hepatocyte differentiation, respectively. Non-inflamed tumors showed higher enhancement on the hepatobiliary-phase of gadolinium-ethoxybenzyl-diethylenetriamine (Gd-EOB-DTPA)-enhanced magnetic resonance imaging (MRI) compared to inflamed tumors. HCCs classified as inflamed class are revealed to have high numbers of CD3+, CD4+, and CD8+ tumor infiltrating lymphocytes on immunostaining. This class is associated with increased expression of anti-epithelial cell adhesion molecule (EpCAM) and FOXM1 accompanied by upregulation of genes related to interferon-gamma signaling, dendritic cell migration, regulatory T cells and MDSC activation and recognized as low enhancement nodule on Gd-EOB-DTPA-enhanced MRI. Conclusion Heterogeneity of tumor traits and TME was observed in HCC with Wnt/β-catenin mutation. The potential was indicated that tumor traits and TME are determined not only by the activation of the HNF4A but also by FOXM1, both of which are downstream transcription factor of the Wnt/β-catenin signaling pathway.
DOI: 10.6084/m9.figshare.24146292.v1
title: Supplementary Material for: Two distinct characteristics of immune microenvironment in human hepatocellular carcinoma with Wnt/β-catenin mutations

description: Introduction Immunotherapy is becoming a promising approach for unresectable-hepatocellular carcinoma (HCC); the anti-tumor response is affected by the tumor microenvironment (TME). Although Wnt/β-catenin mutations are reported to cause non-inflamed phenotype, their role on TME remains controversial. We aimed to clarify the heterogeneity of immunophenotype in HCC with Wnt/β-catenin mutations. Methods This study includes 152 resected HCCs; mutations in the catenin beta-1, adenomatous polyposis coli, or AXIN1, or AXIN2 genes were defined as Wnt/β-catenin mutations. With hierarchical cluster analyses, TME were classified into inflamed or non-inflamed classes based on the gene expressions associated with T-cell activation. Expression profiles of molecules related to cell differentiation and biliary-stem cell markers were compared between the TME classes to investigate whether differences in tumor traits were associated with TME. Results Forty of 152 (26.3%) HCCs carried the Wnt/β-catenin mutations. Of these, 33 were classified as non-inflamed (33/40, 82.5%) and 7 as inflamed (7/40, 17.5%). Non-inflamed class was characterized by low number of CD3+, CD4+, and CD8+ cells on immunostaining, and high mRNA expressions of AXIN2 and GLUL, which are involved in the canonical Wnt/β-catenin signaling and hepatocyte differentiation, respectively. Non-inflamed tumors showed higher enhancement on the hepatobiliary-phase of gadolinium-ethoxybenzyl-diethylenetriamine (Gd-EOB-DTPA)-enhanced magnetic resonance imaging (MRI) compared to inflamed tumors. HCCs classified as inflamed class are revealed to have high numbers of CD3+, CD4+, and CD8+ tumor infiltrating lymphocytes on immunostaining. This class is associated with increased expression of anti-epithelial cell adhesion molecule (EpCAM) and FOXM1 accompanied by upregulation of genes related to interferon-gamma signaling, dendritic cell migration, regulatory T cells and MDSC activation and recognized as low enhancement nodule on Gd-EOB-DTPA-enhanced MRI. Conclusion Heterogeneity of tumor traits and TME was observed in HCC with Wnt/β-catenin mutation. The potential was indicated that tumor traits and TME are determined not only by the activation of the HNF4A but also by FOXM1, both of which are downstream transcription factor of the Wnt/β-catenin signaling pathway.
DOI: 10.5281/zenodo.8333255
title: A new optical practice as an effective alternative to insecticides for controlling highly resistant thrips

description: The documents are raw data for an article entitled "<strong>A new optical practice as an effective alternative to insecticides for controlling highly resistant thrips</strong>", including the original data of Bioassy, Megalurothrips usitatus occurrence rate, RT-qPCR, standard curves, Thrips palmi occurrence rate, and yield and fruit shape of Cowpea and Hami melon.
DOI: 10.5281/zenodo.8333254
title: A new optical practice as an effective alternative to insecticides for controlling highly resistant thrips

description: The documents are raw data for an article entitled "<strong>A new optical practice as an effective alternative to insecticides for controlling highly resistant thrips</strong>", including the original data of Bioassy, Megalurothrips usitatus occurrence rate, RT-qPCR, standard curves, Thrips palmi occurrence rate, and yield and fruit shape of Cowpea and Hami melon.
DOI: 10.6084/m9.figshare.24145827
title: 2systemPET_Section3.3.3.zip

description: Data for Section3.3.3.
DOI: 10.6084/m9.figshare.24145827.v1
title: 2systemPET_Section3.3.3.zip

description: Data for Section3.3.3.
DOI: 10.6084/m9.figshare.24145965
title: ClearMind_Section3.3.2.root

description: Data for Section3.3.2
DOI: 10.6084/m9.figshare.24145965.v1
title: ClearMind_Section3.3.2.root

description: Data for Section3.3.2
DOI: 10.17632/vtt9tg8pk4.1
title: 3D LiDAR and Photogrammetry Scans of a Stilt House in Tai O Village - 2022 - Case 941756

description: This data includes a point cloud file from a combined photogrammetric and LiDAR scan of a stilt house in Tai O Village. The house is designated "Case 941756" in the research project record. Researchers collected the scan using a single, approximately 10 minute walk-through of the house with the Leica-brand BLK2Go model 3D environment scanner. The scan describes the interior and partial exterior of a stilt house in high detail and color. Please note the pointcloud dataset is decimated to a voxel size of 5 millimeters. Full-resolution data is available upon request. The data provides clear enough rendering of the physical conditions of the house to allow interpretation of the scan into description of the house's construction, contents, and spatial use. The data is available under embargo of one year to protect the personal information of residents of the house, provided for purposes of digital conservation of the building, and for interpretation of the house's physical conditions and interior contents through further research. More detailed information on the dataset, including the date the scan was conducted, the location of the house, and related interview and survey datasets are available upon reviewed request.
DOI: 10.17632/t7txdxwvkj.1
title: The Spread of Interferon-γ in Melanomas is Highly Spatially Confined, Driving Non-Genetic Variability in Tumor Cells

description: This is the raw source data that was used to generate figures for the above publication by Centofanti E., Wang C., and Iyer S., et al. It consists of both flow cytometry data corresponding to Figures 2 and 4, Supplementary Figures 2 and 4; and microscopy data corresponding to Figure 3 and Supplementary Figure 3. Full description of how the data were analyzed is given in the methods and figure legends of the publication. All other data from the manuscript is previously published, and accessible via the relevant citations.
DOI: 10.17632/hfwz2fdypg.1
title: JDS miRNA supplemental Figure S8

description: sPLS-DA approach for the selection of the best combination of miRNAs for the prediction of Subclinical endometritis in dairy cows.
DOI: 10.17632/hfwz2fdypg.2
title: JDS miRNA supplemental Figure S8

description: Correlation circle plot representing the miRNAs selected by sPLS-DA performed on the 800 miRNAs detected in plasma
DOI: 10.48420/24138876
title: Optimising the delivery of breast cancer risk assessment for women aged 30–39 years: A qualitative study of women’s views - framework matrices

description: This dataset comprises of the 8 framework matrices which support the themes described in the paper 'Optimising the delivery of breast cancer risk assessment for women aged 30–39 years: A qualitative study of women’s views'. The green text at the top of each cell is the author's summary of the data. Underlining indicates verbatim text. References to potentially interesting quotations are highlighted within the cells of the matrices using Q.
DOI: 10.48420/24138876.v1
title: Optimising the delivery of breast cancer risk assessment for women aged 30–39 years: A qualitative study of women’s views - framework matrices

description: This dataset comprises of the 8 framework matrices which support the themes described in the paper 'Optimising the delivery of breast cancer risk assessment for women aged 30–39 years: A qualitative study of women’s views'. The green text at the top of each cell is the author's summary of the data. Underlining indicates verbatim text. References to potentially interesting quotations are highlighted within the cells of the matrices using Q.
DOI: 10.6084/m9.figshare.24145539
title: Data and R code from Davison <i>et al</i>. "Niche types and community assembly" Ecology Letters

description: Description of the data collection and workflowThe data collection includes 4 R scripts and 4 data sources (3 .csv files and 1 RData object). In combination, the R scripts and data objects can be used to replicate the analyses and figures in Davison et al. "Niche types and community assembly" Ecology Letters. The R scripts call the data sources (which need to be present in the working directory) and should be run in series: step1-&gt;step4. However, because some analytical steps are time consuming, the script includes the possibility to save the output of a step as an RData object that can be loaded at the beginning of the following step. It is also possible to load the RData object 'plottingdata.RData', included in the collection, in order to move directly to the analyses and plotting in step 4 without needing to complete steps 1-3.File contents<i>R scripts</i>Rscript_calculate_niches_step1: Uses AMF communty data and environmental metadata to estimate niche space for AMF taxa (VT).Rscript_analyse_niche_overlap_step2: estimates niche overlap between pairs of VT.RScript_generate_randomisations_step3: implements a stratified randomisation of the AMF community data.RScript_manuscript_analyses_figures_step4: estimates correlations between niche types/axes and models differences in community-level niche differentiation. Plots correlation heatmaps and boxplots.<br><i>Data sources</i>AMFcomm_shared: normalised AMF community data from Davison et al 2021 https://doi.org/10.1111/nph.17240 for use in niche estimation.AMFcomm_shared<i>_</i>raw: raw AMF community data (read counts) from Davison et al 2021 https://doi.org/10.1111/nph.17240 for use in randomisation.plottingdata.RData: data objects including VT niche differentiation estimates and randomised community data matrices for direct use in analysis and plotting (i.e., RScript_manuscript_analyses_figures_step4).meta_shared: environmental meta data from sampling points for use in defining and estimating niche space among VT; and for stratifying randomisation. Soil and climatic variables are taken from Davison <i>et al</i>. (2021) https://doi.org/10.1111/nph.17240; fungal community composition (fungal MDS1 and fungal MDS2) are taken from Vasar <i>et al</i>. (2022) https://doi.org/10.1111/geb.13487; prokaryotic community composition (prokaryotic MDS1 and prokaryotic MDS2) are taken from Vasar <i>et al</i>. (2022) https://doi.org/10.1111/geb.13487; plant community composition (plant MDS1 and plant MDS2) and read counts (bires) are taken from Vasar <i>et al</i>. (2023) https://doi.org/10.3389/fpls.2023.1106617. Columns Olson_REALM and Olson_BIOME_NAME define biogeographic realms and biomes according to Dinerstein <i>et al</i>. 2017 https://doi.org/10.1093/biosci/bix014.<br><br><br><br>
DOI: 10.34740/kaggle/dsv/6477164
title: Egypt Gold Prices | Daily Updated
DOI: 10.6084/m9.figshare.22723315
title: Table S1 Registration numbers and GenBank accession numbers for <i>Missulena </i>sequences included in this study

description: Details for all new sequences and those obtained from GenBank used in Figure S1.
DOI: 10.6084/m9.figshare.22723315.v1
title: Table S1 Registration numbers and GenBank accession numbers for <i>Missulena </i>sequences included in this study

description: Details for all new sequences and those obtained from GenBank used in Figure S1.