cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3555747
title: Appendix C. Percentage of seeds consumed on induced vs. control plants by each seed predator.

description: Percentage of seeds consumed on induced vs. control plants by each seed predator.
DOI: 10.6084/m9.figshare.3555747.v1
title: Appendix C. Percentage of seeds consumed on induced vs. control plants by each seed predator.

description: Percentage of seeds consumed on induced vs. control plants by each seed predator.
DOI: 10.6084/m9.figshare.3555741
title: Appendix D. Isolated fitness impacts of leaf herbivory on 14 Oenothera biennis genotypes.

description: Isolated fitness impacts of leaf herbivory on 14 Oenothera biennis genotypes.
DOI: 10.6084/m9.figshare.3555741.v1
title: Appendix D. Isolated fitness impacts of leaf herbivory on 14 Oenothera biennis genotypes.

description: Isolated fitness impacts of leaf herbivory on 14 Oenothera biennis genotypes.
DOI: 10.6084/m9.figshare.3555738
title: Appendix E. Ellagitannin characterization.

description: Ellagitannin characterization.
DOI: 10.6084/m9.figshare.3555735
title: Appendix A. Information on genetic relatedness of genotypes used in the greenhouse study.

description: Information on genetic relatedness of genotypes used in the greenhouse study.
DOI: 10.6084/m9.figshare.3555735.v1
title: Appendix A. Information on genetic relatedness of genotypes used in the greenhouse study.

description: Information on genetic relatedness of genotypes used in the greenhouse study.
DOI: 10.6084/m9.figshare.3555732
title: Appendix B. Tissue culture methods.

description: Tissue culture methods.
DOI: 10.6084/m9.figshare.3555732.v1
title: Appendix B. Tissue culture methods.

description: Tissue culture methods.
DOI: 10.6084/m9.figshare.3555729
title: Appendix C. Soil moisture differences among the watering treatments.

description: Soil moisture differences among the watering treatments.
DOI: 10.6084/m9.figshare.3555729.v1
title: Appendix C. Soil moisture differences among the watering treatments.

description: Soil moisture differences among the watering treatments.
DOI: 10.6084/m9.figshare.3555726
title: Appendix D. Independent and interactive effect of water amount and frequency on photosynthesis, root biomass, root:shoot, root 0-30 biomass, root:root30, and number of buds.

description: Independent and interactive effect of water amount and frequency on photosynthesis, root biomass, root:shoot, root 0-30 biomass, root:root30, and number of buds.
DOI: 10.6084/m9.figshare.3555726.v1
title: Appendix D. Independent and interactive effect of water amount and frequency on photosynthesis, root biomass, root:shoot, root 0-30 biomass, root:root30, and number of buds.

description: Independent and interactive effect of water amount and frequency on photosynthesis, root biomass, root:shoot, root 0-30 biomass, root:root30, and number of buds.
DOI: 10.6084/m9.figshare.3555723
title: Appendix E. Three-way interactions between water amount, frequency, and genotype on recovery of photosynthesis and shoot biomass.

description: Three-way interactions between water amount, frequency, and genotype on recovery of photosynthesis and shoot biomass.
DOI: 10.6084/m9.figshare.3555723.v1
title: Appendix E. Three-way interactions between water amount, frequency, and genotype on recovery of photosynthesis and shoot biomass.

description: Three-way interactions between water amount, frequency, and genotype on recovery of photosynthesis and shoot biomass.
DOI: 10.6084/m9.figshare.3555720
title: Appendix F. Trait means for each genotype.

description: Trait means for each genotype.
DOI: 10.6084/m9.figshare.3555717
title: Appendix G. Correlation of traits.

description: Correlation of traits.
DOI: 10.6084/m9.figshare.3555714
title: Appendix A. Figure showing the planting design and ANOVA table for the temporal change in the magnitude of overyielding.

description: Figure showing the planting design and ANOVA table for the temporal change in the magnitude of overyielding.
DOI: 10.6084/m9.figshare.3555714.v1
title: Appendix A. Figure showing the planting design and ANOVA table for the temporal change in the magnitude of overyielding.

description: Figure showing the planting design and ANOVA table for the temporal change in the magnitude of overyielding.
DOI: 10.6084/m9.figshare.3555711
title: Appendix B. Allometric relationships of total leaf dry mass used as a proxy for litter production.

description: Allometric relationships of total leaf dry mass used as a proxy for litter production.
DOI: 10.6084/m9.figshare.3555705
title: Appendix C. Supplementary methods, relative strength of evidence, and goodness of fit for the growth models.

description: Supplementary methods, relative strength of evidence, and goodness of fit for the growth models.
DOI: 10.6084/m9.figshare.3555702
title: Supplement 1. R code for the SES (standardized effect sizes) bootstrapping procedures and the hierarchy of linear mixed models of individual tree growth.

description: File List BootstrapSES.R: R code demonstrating how to compute diversity effects as standardized effect size (SES) following Potvin and Gotelli (2008) for both (i) plot-level overyielding and (ii) comparison among canopy statuses.<br> (md5: 0b9c6fc3752d601e7660515eb0505159) MultilevelModeling.R: R code for fitting and comparing the relative support for a hierarchy of linear-mixed models of individual tree growth. R code demonstrating how to compute confidence intervals with a bias-corrected bootstrap method.<br> (md5: c73e3dec4e1059c7c518fe1a07a416fa) Description BootstrapSES.R generates random data conforming to our experimental design (part 0) and tests for overyielding (part 1) using our modified version of the bootstrap methods developed by Potvin and Gotelli (2008). The bootstrap procedure is then used to compare the magnitude of overyielding among canopy statuses (part 2). Part 1 and part 2 could be directly applied to any data.frame containing columns similar to that of “data”, which is fully described at the end of part 0. MultilevelModeling.R requires the lme4 package to fit linear-mixed models. First, methods are defined to generate random tree growth data (simulateData()), to perform bootstrap likelihood ratio tests (bootLRT()), and to compute confidence intervals following a bias-corrected percentile method (see Efron and Tibishrani, 1986; BCconf()). The rest of the code generates random data, fits a hierarchy of linear-mixed model of tree growth, compares the models based on AIC and computes confidence intervals for the most complex example model.
DOI: 10.6084/m9.figshare.3555699
title: Appendix A. Table showing soil characteristics (0–15 cm) surrounding target trees within the three stands in La Selva, Costa Rica.

description: Table showing soil characteristics (0–15 cm) surrounding target trees within the three stands in La Selva, Costa Rica.
DOI: 10.6084/m9.figshare.3555696
title: Appendix B. Table showing mass-based and leaf area-based N and P concentrations in live and senesced Pentaclethra macroloba leaves (proficiency) by soil P fertility in La Selva, Costa Rica.

description: Table showing mass-based and leaf area-based N and P concentrations in live and senesced Pentaclethra macroloba leaves (proficiency) by soil P fertility in La Selva, Costa Rica.
DOI: 10.6084/m9.figshare.3555696.v1
title: Appendix B. Table showing mass-based and leaf area-based N and P concentrations in live and senesced Pentaclethra macroloba leaves (proficiency) by soil P fertility in La Selva, Costa Rica.

description: Table showing mass-based and leaf area-based N and P concentrations in live and senesced Pentaclethra macroloba leaves (proficiency) by soil P fertility in La Selva, Costa Rica.
DOI: 10.6084/m9.figshare.3555693
title: Appendix C. Figure showing leaf-area-based senesced-leaf P and N an live-leaf P and N in P. macroloba in fruiting and non-fruiting trees as a function of tree-level soil P in La Selva, Costa Rica.

description: Figure showing leaf-area-based senesced-leaf P and N an live-leaf P and N in P. macroloba in fruiting and non-fruiting trees as a function of tree-level soil P in La Selva, Costa Rica.
DOI: 10.6084/m9.figshare.3555687
title: Appendix A. Methods for delineating individual tree crowns and calculating height change.

description: Methods for delineating individual tree crowns and calculating height change.
DOI: 10.6084/m9.figshare.3555687.v1
title: Appendix A. Methods for delineating individual tree crowns and calculating height change.

description: Methods for delineating individual tree crowns and calculating height change.
DOI: 10.6084/m9.figshare.3555681
title: Appendix B. A histogram with the year of the last diameter measurement for the 121 LiDAR tall trees (LTTs) tracked in the field.

description: A histogram with the year of the last diameter measurement for the 121 LiDAR tall trees (LTTs) tracked in the field.
DOI: 10.6084/m9.figshare.3555681.v1
title: Appendix B. A histogram with the year of the last diameter measurement for the 121 LiDAR tall trees (LTTs) tracked in the field.

description: A histogram with the year of the last diameter measurement for the 121 LiDAR tall trees (LTTs) tracked in the field.
DOI: 10.6084/m9.figshare.3555678
title: Supplementary Material for: Neutrophil Gelatinase-Associated Lipocalin as a Diagnostic Marker for Acute Kidney Injury in Oliguric Critically Ill Patients: A Post-Hoc Analysis

description: <strong><em>Background:</em></strong> Oliguria occurs frequently in critically ill patients, challenging clinicians to distinguish functional adaptation from serum-creatinine-defined acute kidney injury (AKI<sub>sCr</sub>). We investigated neutrophil gelatinase-associated lipocalin (NGAL)'s ability to differentiate between these 2 conditions. <b><i>Methods:</i></b> This is a post-hoc analysis of a prospective cohort of adult critically ill patients. Patients without oliguria within the first 6 h of admission were excluded. Plasma and urinary NGAL were measured at 4 h after admission. AKI<sub>sCr</sub> was defined using the AKI network criteria with pre-admission serum creatinine or lowest serum creatinine value during the admission as the baseline value. Hazard ratios for AKI<sub>sCr</sub> occurrence within 72 h were calculated using Cox regression and adjusted for risk factors such as sepsis, pre-admission serum creatinine, and urinary output. Positive predictive values (PPV) and negative predictive values (NPV) were calculated for the optimal cutoffs for NGAL. <b><i>Results:</i></b> Oliguria occurred in 176 patients, and 61 (35%) patients developed AKI<sub>sCr</sub>. NGAL was a predictor for AKI<sub>sCr</sub> in univariate and multivariate analysis. When NGAL was added to a multivariate model including sepsis, pre-admission serum creatinine and lowest hourly urine output, it outperformed the latter model (plasma p = 0.001; urinary p = 0.048). Cutoff values for AKI<sub>sCr</sub> were 280 ng/ml for plasma (PPV 80%; NPV 79%), and 250 ng/ml for urinary NGAL (PPV 58%; NPV 78%). <b><i>Conclusions:</i></b> NGAL can be used to distinguish oliguria due to the functional adaptation from AKI<sub>sCr</sub>, directing resources to patients more likely to develop AKI<sub>sCr</sub>.
DOI: 10.6084/m9.figshare.3555678.v1
title: Supplementary Material for: Neutrophil Gelatinase-Associated Lipocalin as a Diagnostic Marker for Acute Kidney Injury in Oliguric Critically Ill Patients: A Post-Hoc Analysis

description: <strong><em>Background:</em></strong> Oliguria occurs frequently in critically ill patients, challenging clinicians to distinguish functional adaptation from serum-creatinine-defined acute kidney injury (AKI<sub>sCr</sub>). We investigated neutrophil gelatinase-associated lipocalin (NGAL)'s ability to differentiate between these 2 conditions. <b><i>Methods:</i></b> This is a post-hoc analysis of a prospective cohort of adult critically ill patients. Patients without oliguria within the first 6 h of admission were excluded. Plasma and urinary NGAL were measured at 4 h after admission. AKI<sub>sCr</sub> was defined using the AKI network criteria with pre-admission serum creatinine or lowest serum creatinine value during the admission as the baseline value. Hazard ratios for AKI<sub>sCr</sub> occurrence within 72 h were calculated using Cox regression and adjusted for risk factors such as sepsis, pre-admission serum creatinine, and urinary output. Positive predictive values (PPV) and negative predictive values (NPV) were calculated for the optimal cutoffs for NGAL. <b><i>Results:</i></b> Oliguria occurred in 176 patients, and 61 (35%) patients developed AKI<sub>sCr</sub>. NGAL was a predictor for AKI<sub>sCr</sub> in univariate and multivariate analysis. When NGAL was added to a multivariate model including sepsis, pre-admission serum creatinine and lowest hourly urine output, it outperformed the latter model (plasma p = 0.001; urinary p = 0.048). Cutoff values for AKI<sub>sCr</sub> were 280 ng/ml for plasma (PPV 80%; NPV 79%), and 250 ng/ml for urinary NGAL (PPV 58%; NPV 78%). <b><i>Conclusions:</i></b> NGAL can be used to distinguish oliguria due to the functional adaptation from AKI<sub>sCr</sub>, directing resources to patients more likely to develop AKI<sub>sCr</sub>.
DOI: 10.6084/m9.figshare.3555675
title: Appendix C. A table describing the annual mean mortality across different habitats at La Selva.

description: A table describing the annual mean mortality across different habitats at La Selva.
DOI: 10.6084/m9.figshare.3555675.v1
title: Appendix C. A table describing the annual mean mortality across different habitats at La Selva.

description: A table describing the annual mean mortality across different habitats at La Selva.
DOI: 10.6084/m9.figshare.3555672
title: Appendix A. Results of ANOVA testing for fertilizer and removal effects on plant community variables.

description: Results of ANOVA testing for fertilizer and removal effects on plant community variables.
DOI: 10.6084/m9.figshare.3555672.v1
title: Appendix A. Results of ANOVA testing for fertilizer and removal effects on plant community variables.

description: Results of ANOVA testing for fertilizer and removal effects on plant community variables.
DOI: 10.6084/m9.figshare.3555663
title: Appendix B. Effect of fertilizer treatments on cover of Empetrum and Deschampsia.

description: Effect of fertilizer treatments on cover of Empetrum and Deschampsia.
DOI: 10.6084/m9.figshare.3555663.v1
title: Appendix B. Effect of fertilizer treatments on cover of Empetrum and Deschampsia.

description: Effect of fertilizer treatments on cover of Empetrum and Deschampsia.
DOI: 10.6084/m9.figshare.3555654
title: Appendix C. Results of ANOVA testing for fertilizer and Empetrum effects on the remainder of the plant community.

description: Results of ANOVA testing for fertilizer and Empetrum effects on the remainder of the plant community.
DOI: 10.6084/m9.figshare.3555654.v1
title: Appendix C. Results of ANOVA testing for fertilizer and Empetrum effects on the remainder of the plant community.

description: Results of ANOVA testing for fertilizer and Empetrum effects on the remainder of the plant community.
DOI: 10.6084/m9.figshare.3555651
title: Appendix D. Results of ANOVA testing for fertilizer and Deschampsia effects on the remainder of the plant community.

description: Results of ANOVA testing for fertilizer and Deschampsia effects on the remainder of the plant community.
DOI: 10.6084/m9.figshare.3555651.v1
title: Appendix D. Results of ANOVA testing for fertilizer and Deschampsia effects on the remainder of the plant community.

description: Results of ANOVA testing for fertilizer and Deschampsia effects on the remainder of the plant community.
DOI: 10.6084/m9.figshare.3555648
title: Appendix E. Results of ANOVA testing for fertilizer and removal effects on soil abiotic variables.

description: Results of ANOVA testing for fertilizer and removal effects on soil abiotic variables.
DOI: 10.6084/m9.figshare.3555648.v1
title: Appendix E. Results of ANOVA testing for fertilizer and removal effects on soil abiotic variables.

description: Results of ANOVA testing for fertilizer and removal effects on soil abiotic variables.
DOI: 10.6084/m9.figshare.3555642
title: Appendix F. Effects of fertilizer treatments on soil chemical properties.

description: Effects of fertilizer treatments on soil chemical properties.
DOI: 10.6084/m9.figshare.3555642.v1
title: Appendix F. Effects of fertilizer treatments on soil chemical properties.

description: Effects of fertilizer treatments on soil chemical properties.
DOI: 10.6084/m9.figshare.3555639
title: Appendix G. Results of ANOVA testing for fertilizer and removal effects on the soil microbial community.

description: Results of ANOVA testing for fertilizer and removal effects on the soil microbial community.
DOI: 10.6084/m9.figshare.3555639.v1
title: Appendix G. Results of ANOVA testing for fertilizer and removal effects on the soil microbial community.

description: Results of ANOVA testing for fertilizer and removal effects on the soil microbial community.
DOI: 10.6084/m9.figshare.3555636
title: Appendix A. Polynomial regression analysis and data values showing the relationship of alkalinity to salinity in Chesapeake Bay.

description: Polynomial regression analysis and data values showing the relationship of alkalinity to salinity in Chesapeake Bay.
DOI: 10.6084/m9.figshare.3555636.v1
title: Appendix A. Polynomial regression analysis and data values showing the relationship of alkalinity to salinity in Chesapeake Bay.

description: Polynomial regression analysis and data values showing the relationship of alkalinity to salinity in Chesapeake Bay.
DOI: 10.6084/m9.figshare.3555633
title: Appendix A. Derivation of Δ, details of MCMC, and plots of posterior distributions for all experiments detailed in Table 3.

description: Derivation of Δ, details of MCMC, and plots of posterior distributions for all experiments detailed in Table 3.
DOI: 10.6084/m9.figshare.3555633.v1
title: Appendix A. Derivation of Δ, details of MCMC, and plots of posterior distributions for all experiments detailed in Table 3.

description: Derivation of Δ, details of MCMC, and plots of posterior distributions for all experiments detailed in Table 3.
DOI: 10.6084/m9.figshare.3555627
title: Supplement 1. R code containing the algorithms described in this paper, as applied to the constant, known food scenario.

description: File List deb_mcmc.R (MD5: 24027cecfc5fc9158b906a8a1d96613f) - R code implementing the MCMC itself<br> deb_model.R (MD5: 67486b9d95fe61db1ddb4add2f89a614) - R code specifying the differential equation model<br> deb_plotting.R (MD5: 4d96e43bc3758b76a81a28c2165442a3) - functions for plotting results <br> deb_post_prior.R (MD5: 0244a22b8855fa8401538680126a2343) - R code with implementation of the priors and posterior distribution<br> deb_solver.R (MD5: ced3a9e359d168038c5c57d5aa93f3d3) - R code with functions to solve the differential equations <br> run_mcmc_knowncf.R (MD5: 3b4d3e1f6931b4bff0f55c216756faa3) - R code that calls everything above and performs the MCMC<br> deb_infer.zip (MD5: 5fb070df6d56a385f21d883f38b1972a) - All files at onceDescription The R code in the file run_mcmc_knowncf.R calls the other files to first simulate data with from the model described in the paper with known parameters (implemented in deb_model.R), and then perform Bayesian inference of the parameters using a Metropolis-within-Gibbs type Markov chain Monte Carlo method (described in the Appendices and implemented in deb_mcmc.R) for the likelihood and priors implemented in deb_post_prior.R. The code requires that the PBSddesolve package cran) be installed.
DOI: 10.6084/m9.figshare.3555627.v1
title: Supplement 1. R code containing the algorithms described in this paper, as applied to the constant, known food scenario.

description: File List deb_mcmc.R (MD5: 24027cecfc5fc9158b906a8a1d96613f) - R code implementing the MCMC itself<br> deb_model.R (MD5: 67486b9d95fe61db1ddb4add2f89a614) - R code specifying the differential equation model<br> deb_plotting.R (MD5: 4d96e43bc3758b76a81a28c2165442a3) - functions for plotting results <br> deb_post_prior.R (MD5: 0244a22b8855fa8401538680126a2343) - R code with implementation of the priors and posterior distribution<br> deb_solver.R (MD5: ced3a9e359d168038c5c57d5aa93f3d3) - R code with functions to solve the differential equations <br> run_mcmc_knowncf.R (MD5: 3b4d3e1f6931b4bff0f55c216756faa3) - R code that calls everything above and performs the MCMC<br> deb_infer.zip (MD5: 5fb070df6d56a385f21d883f38b1972a) - All files at onceDescription The R code in the file run_mcmc_knowncf.R calls the other files to first simulate data with from the model described in the paper with known parameters (implemented in deb_model.R), and then perform Bayesian inference of the parameters using a Metropolis-within-Gibbs type Markov chain Monte Carlo method (described in the Appendices and implemented in deb_mcmc.R) for the likelihood and priors implemented in deb_post_prior.R. The code requires that the PBSddesolve package cran) be installed.
DOI: 10.6084/m9.figshare.3555624
title: Appendix A. Additional details on methods used to determine breeding status of territorial Ovenbirds, invertebrate sampling design, and statistical analyses.

description: Additional details on methods used to determine breeding status of territorial Ovenbirds, invertebrate sampling design, and statistical analyses.
DOI: 10.6084/m9.figshare.3555624.v1
title: Appendix A. Additional details on methods used to determine breeding status of territorial Ovenbirds, invertebrate sampling design, and statistical analyses.

description: Additional details on methods used to determine breeding status of territorial Ovenbirds, invertebrate sampling design, and statistical analyses.
DOI: 10.6084/m9.figshare.3555621
title: Appendix B. Results from the multiple comparison analyses testing for year-specific treatment effects and figures presenting mean abundance and biomass of Coleoptera and Gastropoda for each year and habitat type and abundance between skid trails and inter-trail forest within treated plots.

description: Results from the multiple comparison analyses testing for year-specific treatment effects and figures presenting mean abundance and biomass of Coleoptera and Gastropoda for each year and habitat type and abundance between skid trails and inter-trail forest within treated plots.
DOI: 10.6084/m9.figshare.3555621.v1
title: Appendix B. Results from the multiple comparison analyses testing for year-specific treatment effects and figures presenting mean abundance and biomass of Coleoptera and Gastropoda for each year and habitat type and abundance between skid trails and inter-trail forest within treated plots.

description: Results from the multiple comparison analyses testing for year-specific treatment effects and figures presenting mean abundance and biomass of Coleoptera and Gastropoda for each year and habitat type and abundance between skid trails and inter-trail forest within treated plots.
DOI: 10.6084/m9.figshare.3555618
title: Appendix A. Details on statistical methods with appropriate references, results of analyses of variation in tail length at metamorph emergence, a table detailing the structure of all mixed models used in the paper, and four figures showing variation in metamorph tail length, how tail length at emergence was affected by interactions between age at metamorphosis and hatching age and predator treatment, and how larval resources affected the amount of time metamorphs needed to resorb the tail...

description: Details on statistical methods with appropriate references, results of analyses of variation in tail length at metamorph emergence, a table detailing the structure of all mixed models used in the paper, and four figures showing variation in metamorph tail length, how tail length at emergence was affected by interactions between age at metamorphosis and hatching age and predator treatment, and how larval resources affected the amount of time metamorphs needed to resorb the tail after emergence.