cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13286479.v3
title: A Random Fourier Feature Method for Emulating Computer Models With Gradient Information

description: Computer models with gradient information are increasingly used in engineering and science. The gradient-enhanced Gaussian process emulator can be used for emulating such models. Because the size of the covariance matrix increases proportionally with the dimension of inputs and the sample size, it is computationally challenging to fit such an emulator for large datasets. We propose a random Fourier feature method to mitigate this difficulty. The key idea of the proposed method is to employ random Fourier features to obtain an easily computable, low-dimensional feature representation for shift-invariant kernels involving gradients. The effectiveness of the proposed method is illustrated by several examples.
DOI: 10.15482/usda.adc/1523467
title: Drosophila rhopaloa genome assembly Drho05162011
DOI: 10.15482/usda.adc/1523468
title: Drosophila rhopaloa genome annotations v0.5.3 for genome assembly Drho05162011
DOI: 10.6084/m9.figshare.13341474
title: Bayesian Analysis of Multifidelity Computer Models With Local Features and Nonnested Experimental Designs: Application to the WRF Model

description: Motivated by a multi-fidelity Weather Research and Forecasting (WRF) climate model application where the available simulations are not generated based on hierarchically nested experimental design, we develop a new co-kriging procedure called augmented Bayesian treed co-kriging. The proposed procedure extends the scope of co-kriging in two major ways. We introduce a binary treed partition latent process in the multifidelity setting to account for nonstationary and potential discontinuities in the model outputs at different fidelity levels. Moreover, we introduce an efficient imputation mechanism which allows the practical implementation of co-kriging when the experimental design is nonhierarchically nested by enabling the specification of semiconjugate priors. Our imputation strategy allows the design of an efficient reversible jump Markov chain Monte Carlo implementation that involves collapsed blocks and direct simulation from conditional distributions. We develop the Monte Carlo recursive emulator which provides a Monte Carlo proxy for the full predictive distribution of the model output at each fidelity level, in a computationally feasible manner. The performance of our method is demonstrated on benchmark examples and used for the analysis of a large-scale climate modeling application which involves the WRF model.
DOI: 10.6084/m9.figshare.13341474.v3
title: Bayesian Analysis of Multifidelity Computer Models With Local Features and Nonnested Experimental Designs: Application to the WRF Model

description: Motivated by a multi-fidelity Weather Research and Forecasting (WRF) climate model application where the available simulations are not generated based on hierarchically nested experimental design, we develop a new co-kriging procedure called augmented Bayesian treed co-kriging. The proposed procedure extends the scope of co-kriging in two major ways. We introduce a binary treed partition latent process in the multifidelity setting to account for nonstationary and potential discontinuities in the model outputs at different fidelity levels. Moreover, we introduce an efficient imputation mechanism which allows the practical implementation of co-kriging when the experimental design is nonhierarchically nested by enabling the specification of semiconjugate priors. Our imputation strategy allows the design of an efficient reversible jump Markov chain Monte Carlo implementation that involves collapsed blocks and direct simulation from conditional distributions. We develop the Monte Carlo recursive emulator which provides a Monte Carlo proxy for the full predictive distribution of the model output at each fidelity level, in a computationally feasible manner. The performance of our method is demonstrated on benchmark examples and used for the analysis of a large-scale climate modeling application which involves the WRF model.
DOI: 10.6084/m9.figshare.13341474.v2
title: Bayesian Analysis of Multifidelity Computer Models With Local Features and Nonnested Experimental Designs: Application to the WRF Model

description: Motivated by a multi-fidelity Weather Research and Forecasting (WRF) climate model application where the available simulations are not generated based on hierarchically nested experimental design, we develop a new co-kriging procedure called augmented Bayesian treed co-kriging. The proposed procedure extends the scope of co-kriging in two major ways. We introduce a binary treed partition latent process in the multifidelity setting to account for nonstationary and potential discontinuities in the model outputs at different fidelity levels. Moreover, we introduce an efficient imputation mechanism which allows the practical implementation of co-kriging when the experimental design is nonhierarchically nested by enabling the specification of semiconjugate priors. Our imputation strategy allows the design of an efficient reversible jump Markov chain Monte Carlo implementation that involves collapsed blocks and direct simulation from conditional distributions. We develop the Monte Carlo recursive emulator which provides a Monte Carlo proxy for the full predictive distribution of the model output at each fidelity level, in a computationally feasible manner. The performance of our method is demonstrated on benchmark examples and used for the analysis of a large-scale climate modeling application which involves the WRF model.
DOI: 10.5281/zenodo.5593162
title: A shortcut to calculate SPAM limb-darkening coefficients

description: This repository contains data files and other supplementary material associated with the manuscript entitled "A shortcut to calculate SPAM limb-darkening coefficients", published on the Research Notes of the American Astronomical Society (RNAAS).
DOI: 10.5281/zenodo.5593161
title: A shortcut to calculate SPAM limb-darkening coefficients

description: This repository contains data files and other supplementary material associated with the manuscript entitled "A shortcut to calculate SPAM limb-darkening coefficients", published on the Research Notes of the American Astronomical Society (RNAAS).
DOI: 10.15482/usda.adc/1523469
title: Drosophila ficusphila genome assembly Dfic02082011
DOI: 10.15482/usda.adc/1523470
title: Drosophila ficusphila genome annotations v0.5.3 for genome assembly Dfic02082011
DOI: 10.23708/pdbbqr
title: Analysis of soil samples collected over Huay Ma Nai catchment in Northern Thailand in 2001

description: This dataset has been collected thanks to the long-term partnership with National Park, Wildlife and Plant Conservation Department (DNP), Thailand, which granted the permission for field access, and to the financial, scientific, technical, and/or logistical support of the Multiscale TROPIcal CatchmentS (SNO M-TROPICS; https://mtropics.obs-mip.fr/) critical zone observatory (previously MSEC). The soil samples were taken at different depths and under different vegetation covers at the long-term observatory catchment Huay Ma Nai in northern Thailand in 2001. The dataset holds general physical and chemical parameters of soil samples. Carbon (C), Nitrogen (N), Phosphorus (P) concentrations were assessed. Extractible Fe and Al has been analyzed by dithionite-citrate extractions. Cation exchange capacity (CEC) and grain size distribution were also measured and X-ray crystallography analysis has been conducted. Soil analyses have been carried out at the IRD laboratory in Cayenne, Guyane. The authors acknowledge the financial support of the Institut de Recherche pour le Développement (IRD).
DOI: 10.6084/m9.figshare.14555499
title: 04. BEAST input file generated in BEAUTI

description: BEAST input XML file generated in BEAST.
DOI: 10.6084/m9.figshare.14555478
title: 03. Final annotated tree

description: Final anotated BEAST tree using TreeAnnotator.
DOI: 10.6084/m9.figshare.14555478.v1
title: 03. Final annotated tree

description: Final anotated BEAST tree using TreeAnnotator.
DOI: 10.6084/m9.figshare.14555445
title: 02. Trees produced by BEAST under the relaxed clock model

description: Trees produced by BEAST under the relaxed clock model. Data was partitioned by marker.
DOI: 10.6084/m9.figshare.14555445.v1
title: 02. Trees produced by BEAST under the relaxed clock model

description: Trees produced by BEAST under the relaxed clock model. Data was partitioned by marker.
DOI: 10.6084/m9.figshare.14555424
title: 01. Concatenated alignment

description: Concatenate alignment from five DNA markers: nrITS, matK, rbcL, rpl16, tnrL
DOI: 10.6084/m9.figshare.14555424.v1
title: 01. Concatenated alignment

description: Concatenate alignment from five DNA markers: nrITS, matK, rbcL, rpl16, tnrL
DOI: 10.23708/x8yf1i
title: Analysis of soil samples collected over Huay Ma Nai catchment in Northern Thailand in 2017

description: This dataset has been collected thanks to the long-term partnership with National Park, Wildlife and Plant Conservation Department (DNP), Thailand, which granted the permission for field access, and to the financial, scientific, technical, and/or logistical support of the Multiscale TROPIcal CatchmentS (SNO M-TROPICS; https://mtropics.obs-mip.fr/) critical zone observatory (previously MSEC). The soil samples were taken under different vegetation covers at the long-term observatory catchment Huay Ma Nai in northern Thailand in 2017. This dataset holds some chemical and physical soils properties. Dry combustion analysis (CHN) was used to assess Carbon (C) and Nitrogen (N) concentrations. Fourier-transform infrared (FTIR) spectroscopy was used to measure the signature of the samples in the medium infrared region. Soil analyses have been carried out at the Pôle d’expérimentation et d’analyse des sols et sédiments tropicaux (ALYSÉS). The authors acknowledge the financial support of the Institut de Recherche pour le Développement (IRD).
DOI: 10.5281/zenodo.5517857
title: Forest defoliator outbreaks disrupt nutrient cycling in northern waters

description: Datasets for manuscript Forest defoliator outbreaks alter nutrient cycling in northern waters. IO_df is the main insect outbreak dataframe used to generate the bulk of the figures and results. It contains measures of monthly lake chemistry, insect disturbance, and catchment characteristics. Defoliator_Bark-Wood-Beetle_df is used to generate figure S1 and contains yearly measures of defoliator and bark/wood beetle outbreaks. ndvi_lai_data is used to generate figure S6 and contains the relationship between MOIDS LAI and Landsat NDVI. Outbreak_History is used to generate figure 5 and is a record of catchment-level disturbances in our study region.
DOI: 10.5281/zenodo.5517856
title: Forest defoliator outbreaks disrupt nutrient cycling in northern waters

description: Datasets for manuscript Forest defoliator outbreaks alter nutrient cycling in northern waters. IO_df is the main insect outbreak dataframe used to generate the bulk of the figures and results. It contains measures of monthly lake chemistry, insect disturbance, and catchment characteristics. Defoliator_Bark-Wood-Beetle_df is used to generate figure S1 and contains yearly measures of defoliator and bark/wood beetle outbreaks. ndvi_lai_data is used to generate figure S6 and contains the relationship between MOIDS LAI and Landsat NDVI. Outbreak_History is used to generate figure 5 and is a record of catchment-level disturbances in our study region.
DOI: 10.23708/pbyfao
title: Dataset relating soil organic content and caesium-137 activities in the Houay Pano catchment of northern Laos over 42 years (1963-2015)

description: This dataset has been collected thanks to the long-term partnership with Department of Agricultural Land Management (DALaM), Lao PDR, which granted the permission for field access, and to the financial, scientific, technical, and/or logistical support of the Multiscale TROPIcal CatchmentS (SNO M-TROPICS; https://mtropics.obs-mip.fr/) critical zone observatory (previously MSEC). The soil samples were taken at different soil depths and under different vegetation covers at the long-term observatory catchment of Houay Pano in Northern Laos between 2000 and 2005. The dataset holds some general soil properties: bulk dry density (cylinder method), total organic carbon concentration (TOC), total nitrogen concentration (TN), 13C/12C and 15N/14N isotope ratios determined by EA-IRMS (dry combustion), radionuclide 137Cs and 210Pbxs activities and Potassium concentration (K) were measured by gamma-ray spectrometry. Soil elemental and isotopic analyses were carried out at iEES Paris laboratory. Radionuclides activities were measured at Laboratoire des Sciences du Climat et de l‘Environnement (LSCE) in Gif-sur-Yvette. The authors acknowledge the financial support of the Institut de Recherche pour le Développement (IRD), of the the French INSU project PNSE 12, and of the FFEM-AFD program
DOI: 10.15482/usda.adc/1523471
title: Drosophila eugracilis genome assembly Deug05112011
DOI: 10.15482/usda.adc/1523472
title: Drosophila eugracilis genome annotations v0.5.3 for genome assembly Deug05112011
DOI: 10.23708/dxdagv
title: Termite mound distribution and size within the Mule Hole long term observatory, Karnataka, India

description: This dataset has been collected thanks to the long-term partnership with Mahatma Gandhi University, India, It holds termite mound distribution (cathedral mounds built by Odontotermes obesus vs. lenticular mounds occupied by a large diversity of organisms) and size within the Mule Hole watershed. Data collected in 2014, 2015, 2016, 2017 and 2018.
DOI: 10.25345/c5vs06
title: MassIVE MSV000088264 - Adducin Regulates Sarcomere Disassembly During Mammalian Cardiomyocyte Mitosis
title: S02196: Group control, IgG S02197: mouse 3 days post MI surgery at age P1 S02198: mouse 3 days post MI surgery at age P7 781478: P1-lysate, lysates from mouse heart at the age of P1, control 781479: P2-lysate, lysates from mouse heart at the age of P21, control 781480: P1-beads, P1 mouse heart lysates bound to Ni-NTA agarose beads without purified adducin complex as baits in Co-IP 781481: P21-beads, P21 mouse heart lysates bound to Ni-NTA agarose beads without purified adducin complex as baits in Co-IP 781482: P1-long adducin, Co-IP of P1 mouse heart lysates by purified full length WT ADD1/ADD3 complex 781483: P21-long adducin, Co-IP of P21 mouse heart lysates by purified full length WT ADD1/ADD3 complex 781484: P1-short adducin, Co-IP of P1 mouse heart lysates by purified short length ADD1 isoform2/ADD3 complex 781485: P21-short adducin, Co-IP of P21 mouse heart lysates by purified short length ADD1 isoform2/ADD3 complex
DOI: 10.6084/m9.figshare.16860238
title: Going for gold: exploring the reach and impact of Gold open access articles in hybrid journals [data set]

description: In 2021, Springer Nature commissioned an analysis of 60,567 articles published in 1,262 of its hybrid journals, measuring reach by the number of downloads and the attention reflected in the Altmetric Attention Score, and impact through the number of citations.<br>This is the data set for the white paper which presents the findings from that analysis, which show a clear advantage in reach and impact for articles published OA in hybrid journals compared to non-OA articles in the same journals, and for the first time also an advantage for full (Gold) OA articles compared to subscription articles where an earlier article version (such as an accepted manuscript (AM) or preprint) has been self-archived in an OA repository. <br>White paper: https://figshare.com/articles/journal_contribution/Going_for_gold_exploring_the_reach_and_impact_of_Gold_open_access_articles_in_hybrid_journals_white_paper_/16860229
DOI: 10.5517/ccdc.csd.cc21l1c2
title: CCDC 1894173: Experimental Crystal Structure Determination

description: Related Article: Maite Perfecto-Irigaray, Garikoitz Beobide, Oscar Castillo, Ivan da Silva, Daniel García-Lojo, Antonio Luque, Ander Mendia, Sonia Pérez-Yáñez|2019|Chem.Commun.|55|5954|doi:10.1039/C9CC00802K
DOI: 10.5281/zenodo.5532918
title: Brazilian Portuguese CHV

description: Part of Brazilian Portuguese CHV
DOI: 10.5281/zenodo.5532917
title: Brazilian Portuguese CHV

description: Part of Brazilian Portuguese CHV
DOI: 10.23708/gvwca0
title: Analysis of earthworm casts and soils collected over Dong Cao catchment in Northern Vietnam in 2016

description: Earthworm casts and their surrounding topsoil were taken in collaboration with the Soils and Fertilizers Research Institute (SFRI) under different vegetation cover at the long term observatory catchment of Dong Cao in Northern Vietnam in 2016. This dataset holds general chemical parameters of soil samples. Dry combustion analysis (CHN) was used to assess organic Carbon (TOC) and Nitrogen (N) concentrations. Natural isotopes Carbon-13 (13C) and Nitrogen (15N) were analyzed by mass spectrometry. Soil analyses have been carried out at the "Pôle d’expérimentation et d’analyse des sols et sédiments tropicaux" (ALYSÉS). The collection of the data was supported by CNRS/INSU (VINAWORM) research program under the framework of the EC2CO program.
DOI: 10.5517/ccdc.csd.cc2764k5
title: CCDC 2061486: Experimental Crystal Structure Determination

description: Related Article: Yan Fan, Zhiming Zeng, Hui Shu, Mingbo Zhou, Ling Xu, Yutao Rao, Tingting Gu, Xu Liang, Weihua Zhu, Jianxin Song|2021|Org.Chem.Front.|8|6080|doi:10.1039/D1QO01161H
DOI: 10.5517/ccdc.csd.cc27ml1j
title: CCDC 2074397: Experimental Crystal Structure Determination

description: Related Article: Hao-Zhao Wei, Yin Wei, Min Shi|2021|Chem.Commun.|57|11201|doi:10.1039/D1CC04826K
DOI: 10.23708/g3hwon
title: Phytoliths in termite mounds and in the soil environment, India, 2017

description: This dataset has been collected thanks to the long-term partnership with Mahatma Gandhi University, India. The dataset holds detailled phytolith counts and statistics.Phytoliths were extracted from termite mounds build by Odontotermes obesus in the Mule Hole long term observatory. Comparison was done between samples collected from the outer-wall of termite mounds and in the soil at 0-5 and 70-120 cm soil layers.
DOI: 10.5281/zenodo.5600087
title: Data from: Saltmarsh vegetation and secured woody debris facilitate mangrove re-colonization

description: Does the presence of saltmarsh vegetation affect the long-term regeneration of the pioneer mangrove species <em>Avicennia germinans</em> in a degraded dwarf forest? Does immobilized coarse woody debris (CWD) affect regeneration similarly? Do larger trees suppress or facilitate intraspecific saplings? The study was conducted in a dwarf mangrove forest in the high intertidal zone on Bragança peninsula in northern Brazil. The spatial patterns of <em>A. germinans</em>, the herbaceous halophyte <em>Sesuvium portulacastrum</em>, and CWD were mapped in three sample plots (each 400 m<sup>2</sup>) during two consecutive vegetation surveys, conducted in 2011 and 2014. Inhomogeneous Poisson and Thomas point-process models were used to assess the distribution of <em>A. germinans</em> life-history stages (seedlings, saplings, and adult dwarf trees), conditioned on the presence of <em>S. portulacastrum</em> and CWD. In addition, intraspecific interactions between trees and regeneration were assessed based on crown projection mapping. Bivariate point pattern analyses were used to assess the dependence of advance regeneration on dwarf <em>A. germinans</em> trees and <em>S. portulacastrum</em>. <em>A. germinans</em> saplings and trees were positively associated with <em>S. portulacastrum</em> and CWD, whereas seedlings were located around tree crowns. The density of fruit-bearing trees was positively associated with sapling density, indicating that regeneration relied on locally dispersed propagules. Herbaceous vegetation and CWD have an important ecological function in degraded mangroves by retaining tidally dispersed propagules. Here, we show that herbaceous vegetation does not suppress the growth of seedlings but facilitates mangrove recolonization. Due to limited tidal dispersal, regeneration relies on local propagule supply. In addition to hydrological restoration, the observed vegetation patterns suggest that, in the absence of propagule-retaining vegetation, restoration of high-intertidal mangroves can be facilitated by establishing nuclei of planted trees and installing secured logs.
description: File 1: Stem coordinates (cm) of A. germinans individuals of different life-history stages in three sample plots (2000 cm x 2000 cm) File 2: Cell center coordinates (cm) of S. portulacastrum patches with a size of 10 cm x 10 cm each within three sample plots File 3: Endpoint coordinates (cm) of straight coarse woody debris segments within three sample plots File 4: Canopy height raster cells of three sample plots File 5: Extent of tree crowns in eight cardinal directions (cm) around stem coordinates in three sample plots with additional height (cm) and presence of fruits (y - yes, n - no) File 6: Stem coordinates (cm), height (cm), and number of internodes of saplings measured in 2014 in three sample plots Time of data collection: January to March 2011 and January to March 2014