cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3544592.v1
title: Appendix A. Mean height, patterns of biomass allocation, leaf area, and light interception per species in each of the three successional stands as well the results Sidak pairwise comparisons between species within stands.

description: Mean height, patterns of biomass allocation, leaf area, and light interception per species in each of the three successional stands as well the results Sidak pairwise comparisons between species within stands.
DOI: 10.6084/m9.figshare.3544589
title: Appendix B. Results of analysis of covariance analyzing species effects on the relationships between daily whole-plant photosynthesis and plant or leaf mass and between leaf light-saturated photosynthesis and leaf nitrogen contents.

description: Results of analysis of covariance analyzing species effects on the relationships between daily whole-plant photosynthesis and plant or leaf mass and between leaf light-saturated photosynthesis and leaf nitrogen contents.
DOI: 10.6084/m9.figshare.3544589.v1
title: Appendix B. Results of analysis of covariance analyzing species effects on the relationships between daily whole-plant photosynthesis and plant or leaf mass and between leaf light-saturated photosynthesis and leaf nitrogen contents.

description: Results of analysis of covariance analyzing species effects on the relationships between daily whole-plant photosynthesis and plant or leaf mass and between leaf light-saturated photosynthesis and leaf nitrogen contents.
DOI: 10.6084/m9.figshare.3544586
title: Appendix A. Environmental characteristics of experimental plots.

description: Environmental characteristics of experimental plots.
DOI: 10.6084/m9.figshare.3544586.v1
title: Appendix A. Environmental characteristics of experimental plots.

description: Environmental characteristics of experimental plots.
DOI: 10.6084/m9.figshare.3544583
title: Appendix B. Heights and rates of growth, survival, and herbivory of seedlings in experimental plots.

description: Heights and rates of growth, survival, and herbivory of seedlings in experimental plots.
DOI: 10.6084/m9.figshare.3544580
title: Appendix A. Linear regressions for the grasses and forbs that were investigated in the grasshopper feeding experiment with respect to the two nonmetric multidimensional scaling axes (NMDS).

description: Linear regressions for the grasses and forbs that were investigated in the grasshopper feeding experiment with respect to the two nonmetric multidimensional scaling axes (NMDS).
DOI: 10.6084/m9.figshare.3544580.v1
title: Appendix A. Linear regressions for the grasses and forbs that were investigated in the grasshopper feeding experiment with respect to the two nonmetric multidimensional scaling axes (NMDS).

description: Linear regressions for the grasses and forbs that were investigated in the grasshopper feeding experiment with respect to the two nonmetric multidimensional scaling axes (NMDS).
DOI: 10.6084/m9.figshare.3544577
title: Appendix A. Effects of various factors on mass of Spodoptera exigua and proteinase inhibitor activity.

description: Effects of various factors on mass of Spodoptera exigua and proteinase inhibitor activity.
DOI: 10.6084/m9.figshare.3544577.v1
title: Appendix A. Effects of various factors on mass of Spodoptera exigua and proteinase inhibitor activity.

description: Effects of various factors on mass of Spodoptera exigua and proteinase inhibitor activity.
DOI: 10.5281/zenodo.4014310
title: Dataset for: Thermofluidic heat exchangers for actuation of transcription in artificial tissues

description: Dataset for: Thermofluidic heat exchangers for actuation of transcription in artificial tissues Daniel C. Corbett1,2, Wesley B. Fabyan1,2, Bagrat Grigoryan3, Colleen E. O’Connor1,2,<br> Fredrik Johansson1,2, Ivan Batalov1,2, Mary C. Regier1,2, Cole A. DeForest1,2,4,<br> Jordan S. Miller3, Kelly R. Stevens1,2,5,6* 1Department of Bioengineering, University of Washington, Seattle, WA 98195, USA. 2Institute for Stem Cell and Regenerative Medicine, Seattle, WA 98195, USA. 3Department<br> of Bioengineering, Rice University, Houston, TX 77005, USA. 4Department of<br> Chemical Engineering, University of Washington, Seattle, WA 98195, USA. 5Department<br> of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195,<br> USA. 6Brotman Baty Institute, University of Washington, Seattle, WA 98195, USA.<br> *Corresponding author. Email: ksteve@uw.edu <br> Spatial patterns of gene expression in living organisms orchestrate cell decisions in development, homeostasis, and disease. However, most methods for reconstructing gene patterning in 3D cell culture and artificial tissues are restricted by patterning depth and scale. We introduce a depth- and scale-flexible method to direct volumetric gene expression patterning in 3D artificial tissues, which we call “heat exchangers for actuation of transcription” (HEAT). This approach leverages fluid-based heat transfer from printed networks in the tissues to activate heat-inducible transgenes expressed by embedded cells. We show that gene expression patterning can be tuned both spatially and dynamically by varying channel network architecture, fluid temperature, fluid flow direction, and stimulation timing in a user-defined manner and maintained in vivo. We apply this approach to activate the 3D positional expression of Wnt ligands and Wnt/-catenin pathway regulators, which are major regulators of development, homeostasis, regeneration, and cancer throughout the animal kingdom.
DOI: 10.5281/zenodo.4014309
title: Dataset for: Thermofluidic heat exchangers for actuation of transcription in artificial tissues

description: Dataset for: Thermofluidic heat exchangers for actuation of transcription in artificial tissues Daniel C. Corbett1,2, Wesley B. Fabyan1,2, Bagrat Grigoryan3, Colleen E. O’Connor1,2,<br> Fredrik Johansson1,2, Ivan Batalov1,2, Mary C. Regier1,2, Cole A. DeForest1,2,4,<br> Jordan S. Miller3, Kelly R. Stevens1,2,5,6* 1Department of Bioengineering, University of Washington, Seattle, WA 98195, USA. 2Institute for Stem Cell and Regenerative Medicine, Seattle, WA 98195, USA. 3Department<br> of Bioengineering, Rice University, Houston, TX 77005, USA. 4Department of<br> Chemical Engineering, University of Washington, Seattle, WA 98195, USA. 5Department<br> of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195,<br> USA. 6Brotman Baty Institute, University of Washington, Seattle, WA 98195, USA.<br> *Corresponding author. Email: ksteve@uw.edu <br> Spatial patterns of gene expression in living organisms orchestrate cell decisions in development, homeostasis, and disease. However, most methods for reconstructing gene patterning in 3D cell culture and artificial tissues are restricted by patterning depth and scale. We introduce a depth- and scale-flexible method to direct volumetric gene expression patterning in 3D artificial tissues, which we call “heat exchangers for actuation of transcription” (HEAT). This approach leverages fluid-based heat transfer from printed networks in the tissues to activate heat-inducible transgenes expressed by embedded cells. We show that gene expression patterning can be tuned both spatially and dynamically by varying channel network architecture, fluid temperature, fluid flow direction, and stimulation timing in a user-defined manner and maintained in vivo. We apply this approach to activate the 3D positional expression of Wnt ligands and Wnt/-catenin pathway regulators, which are major regulators of development, homeostasis, regeneration, and cancer throughout the animal kingdom.
DOI: 10.6084/m9.figshare.3544574
title: Appendix A. Plot locations, species lists and food webs, comparison of consumer/resource models, and tests for apparent competition.

description: Plot locations, species lists and food webs, comparison of consumer/resource models, and tests for apparent competition.
DOI: 10.6084/m9.figshare.3544574.v1
title: Appendix A. Plot locations, species lists and food webs, comparison of consumer/resource models, and tests for apparent competition.

description: Plot locations, species lists and food webs, comparison of consumer/resource models, and tests for apparent competition.
DOI: 10.6084/m9.figshare.3544571
title: Appendix A. Description of experimental lakes.

description: Description of experimental lakes.
DOI: 10.6084/m9.figshare.3544571.v1
title: Appendix A. Description of experimental lakes.

description: Description of experimental lakes.
DOI: 10.6084/m9.figshare.3544568
title: Appendix B. Species abundances and colonist survival.

description: Species abundances and colonist survival.
DOI: 10.6084/m9.figshare.3544568.v1
title: Appendix B. Species abundances and colonist survival.

description: Species abundances and colonist survival.
DOI: 10.6084/m9.figshare.3544565
title: Appendix C. Water chemistry and chlorophyll methods and results.

description: Water chemistry and chlorophyll methods and results.
DOI: 10.6084/m9.figshare.3544565.v1
title: Appendix C. Water chemistry and chlorophyll methods and results.

description: Water chemistry and chlorophyll methods and results.
DOI: 10.6084/m9.figshare.3544562
title: Appendix A. Location, size, and depth of stickleback lakes.

description: Location, size, and depth of stickleback lakes.
DOI: 10.6084/m9.figshare.3544562.v1
title: Appendix A. Location, size, and depth of stickleback lakes.

description: Location, size, and depth of stickleback lakes.
DOI: 10.6084/m9.figshare.3544559
title: Appendix A. Supplemental figures showing the results from the winters of 1994 and 1995.

description: Supplemental figures showing the results from the winters of 1994 and 1995.
DOI: 10.6084/m9.figshare.3544559.v1
title: Appendix A. Supplemental figures showing the results from the winters of 1994 and 1995.

description: Supplemental figures showing the results from the winters of 1994 and 1995.
DOI: 10.6084/m9.figshare.3544556
title: Supplement 1. R code to implement the Metropolis-Hastings algorithm.

description: File List carlson_etal_ecology_supplement_Rscript.txt Description This is a text file containing annotated R code to fit the Bayesian model for the survival function based on the pre-winter and post-winter inverse Gaussian length distributions. The code implements the Metropolis-Hastings algorithm to sample from the posterior distribution of the three parameters of the model. In particular, the output includes posterior samples for parameters “mu” and “phi” (the mean and shape parameter, respectively, of the pre-winter length distribution) and for "alpha" (the parameter of the survival function). These posterior samples can be used, as described in the paper, to plot point and interval estimates for the survival function and for the pre-winter and post-winter length densities.
DOI: 10.6084/m9.figshare.3544553
title: Appendix A. Summary information on three foraging strategies of male California sea lions outfitted with Sea Mammal Research Unit SRDL tags and a photograph of the floating platform and aluminum enclosure used for passive capture of adult male sea lions.

description: Summary information on three foraging strategies of male California sea lions outfitted with Sea Mammal Research Unit SRDL tags and a photograph of the floating platform and aluminum enclosure used for passive capture of adult male sea lions.
DOI: 10.6084/m9.figshare.3544553.v1
title: Appendix A. Summary information on three foraging strategies of male California sea lions outfitted with Sea Mammal Research Unit SRDL tags and a photograph of the floating platform and aluminum enclosure used for passive capture of adult male sea lions.

description: Summary information on three foraging strategies of male California sea lions outfitted with Sea Mammal Research Unit SRDL tags and a photograph of the floating platform and aluminum enclosure used for passive capture of adult male sea lions.
DOI: 10.6084/m9.figshare.3544550
title: Appendix A. Figures showing nine-year records of phytoplankton biomass and Chlsat at eight-day resolution for the 12 North Atlantic bins, mean annual cycles in phytoplankton carbon and Chlsat at eight-day resolution for the 12 North Atlantic bins, and 5° latitude zonal mean values of phytoplankton net specific growth rate during the positive phase of the annual cycle and spring maximum in surface chlorophyll concentration.

description: Figures showing nine-year records of phytoplankton biomass and Chlsat at eight-day resolution for the 12 North Atlantic bins, mean annual cycles in phytoplankton carbon and Chlsat at eight-day resolution for the 12 North Atlantic bins, and 5° latitude zonal mean values of phytoplankton net specific growth rate during the positive phase of the annual cycle and spring maximum in surface chlorophyll concentration.
DOI: 10.6084/m9.figshare.3544547
title: Supplement 1. Data and R script for reproducing the correspondence analysis of raw data and a video file showing the transition from regular to "raw" correspondence analysis (CA-relative to CA-raw).

description: File List CAraw_data.csv<br> CA_raw.R<br> CA_rel_to_raw.swf Description The CAraw_data.csv file is a comma-delimited data file containing the benthic abundance data analyzed in the statistical report.<br> --- Rows are the 13 sampling stations (stations R40 and R42 are references)<br> --- Columns are the 92 species, with abbreviated latin names<br> Note that the first row contains the 92 column names, and the first column the 13 site names. Thus there is one fewer item in the first row, which is convenient for reading with the read.table function in R. The CA_raw.R file is an R script for performing the computations of CA-raw. The CA_rel_to_raw.swf file is a video file showing the transition from CA-relative (the usual form of correspondence analysis) to CA-raw. (This video in shockwave flash format can be opened in a browser such as Firefox).
DOI: 10.6084/m9.figshare.3544547.v1
title: Supplement 1. Data and R script for reproducing the correspondence analysis of raw data and a video file showing the transition from regular to "raw" correspondence analysis (CA-relative to CA-raw).

description: File List CAraw_data.csv<br> CA_raw.R<br> CA_rel_to_raw.swf Description The CAraw_data.csv file is a comma-delimited data file containing the benthic abundance data analyzed in the statistical report.<br> --- Rows are the 13 sampling stations (stations R40 and R42 are references)<br> --- Columns are the 92 species, with abbreviated latin names<br> Note that the first row contains the 92 column names, and the first column the 13 site names. Thus there is one fewer item in the first row, which is convenient for reading with the read.table function in R. The CA_raw.R file is an R script for performing the computations of CA-raw. The CA_rel_to_raw.swf file is a video file showing the transition from CA-relative (the usual form of correspondence analysis) to CA-raw. (This video in shockwave flash format can be opened in a browser such as Firefox).
DOI: 10.6084/m9.figshare.3544544
title: Appendix A. Precision of the Gauss-Hermite quadrature approximation.

description: Precision of the Gauss-Hermite quadrature approximation.
DOI: 10.6084/m9.figshare.3544544.v1
title: Appendix A. Precision of the Gauss-Hermite quadrature approximation.

description: Precision of the Gauss-Hermite quadrature approximation.
DOI: 10.6084/m9.figshare.3544541
title: Appendix B. Approximating the marginal likelihood of models {Φ(t), p(t+h)} and {Φ(t+h), p(t+h)} using a Gauss-Hermite quadrature approximation.

description: Approximating the marginal likelihood of models {Φ(t), p(t+h)} and {Φ(t+h), p(t+h)} using a Gauss-Hermite quadrature approximation.
DOI: 10.6084/m9.figshare.3544538
title: Appendix C. Model selection in the Sociable Weaver and European Dipper case studies.

description: Model selection in the Sociable Weaver and European Dipper case studies.
DOI: 10.6084/m9.figshare.3544535
title: Appendix D. Incorporating individual random effects using program E-SURGE.

description: Incorporating individual random effects using program E-SURGE.
DOI: 10.6084/m9.figshare.3761562.v1594
title: Online Labour Index: Measuring the Online Gig Economy for Policy and Research

description: Data repository for the data underlying the Online Labour Index. See http://ilabour.oii.ox.ac.uk online-labour-index/ for details.
DOI: 10.6084/m9.figshare.3544532
title: Data Paper. Data Paper

description: File List Jena_Biomass_02-08.csv Jena_Community_02-08.csv Description This data set contains species-specific biomass and cover data as well as community leaf area index (LAI) and height from a large grassland biodiversity experiment (Jena Experiment). In this experiment, 82 grassland plots of 20 × 20 m were established from a pool of 60 species belonging to four functional groups (grasses, legumes, and tall and small herbs). In May 2002, varying numbers of plant species were sown into the plots to create a gradient of plant species richness (1, 2, 4, 8, 16, and 60 species) and functional richness (1, 2, 3, and 4 functional groups). Plots were maintained by biannual weeding and mowing. The data set encompasses the 2002–2008 May and August biomass harvests from 3–4 subplots of 0.2 × 0.5 m per experimental plot sorted to species. Moreover, plant species and community cover estimated in an approximately 9-m<sup>2</sup> subplot per plot are included in the data set. Each biomass harvest was accompanied by measurements of vegetation height and LAI per plot. Analyses of the community biomass data have identified species richness as well as functional group composition as important drivers of a positive biodiversity–productivity relationship. The data set can be used to study a variety of questions about how plant community composition and structure responds to changes in species richness and functional diversity over time. Sampling is ongoing, and new data will be added. <i>Key words: biodiversity experiment; functional composition; height; LAI; plant community; species biomass; species cover</i>.
DOI: 10.6084/m9.figshare.3544529
title: Appendix A. A table showing ratios of multigenerational estimates of effective population size for individual populations of chinook salmon.

description: A table showing ratios of multigenerational estimates of effective population size for individual populations of chinook salmon.
DOI: 10.6084/m9.figshare.3544529.v1
title: Appendix A. A table showing ratios of multigenerational estimates of effective population size for individual populations of chinook salmon.

description: A table showing ratios of multigenerational estimates of effective population size for individual populations of chinook salmon.
DOI: 10.6084/m9.figshare.3544526
title: Appendix A. A figure showing water temperatures recorded at the four study sites from November 2007 to August 2008.

description: A figure showing water temperatures recorded at the four study sites from November 2007 to August 2008.
DOI: 10.6084/m9.figshare.3544526.v1
title: Appendix A. A figure showing water temperatures recorded at the four study sites from November 2007 to August 2008.

description: A figure showing water temperatures recorded at the four study sites from November 2007 to August 2008.
DOI: 10.6084/m9.figshare.3544523
title: Appendix A. Sampling localities, equilibrium simulations, and simulations with varying r.

description: Sampling localities, equilibrium simulations, and simulations with varying r.
DOI: 10.6084/m9.figshare.3544520
title: Appendix A. Descriptions of the derivation of likelihood and restricted likelihood functions for an ARMA(p,q) process, including the incorporation of measurement error.

description: Descriptions of the derivation of likelihood and restricted likelihood functions for an ARMA(p,q) process, including the incorporation of measurement error.
DOI: 10.6084/m9.figshare.3544520.v1
title: Appendix A. Descriptions of the derivation of likelihood and restricted likelihood functions for an ARMA(p,q) process, including the incorporation of measurement error.

description: Descriptions of the derivation of likelihood and restricted likelihood functions for an ARMA(p,q) process, including the incorporation of measurement error.
DOI: 10.6084/m9.figshare.3544517
title: Supplement 1. MATLAB and R code for performing ARMA(p,q) model fitting.

description: File List ARMApqREMLfunct.m -- Matlab code for the ARMA likelihood function for REML and ML estimation ARMApq_ME_REMLfunct.m -- Matlab code for the ARMA likelihood function for pseudo-REML and pseudo_ML estimation ARMApqREMLfunct_R.txt -- R code for the ARMA likelihood function for REML and ML estimation Description The ARMApqREMLfunct.m matlab program gives the negative log likelihood function and restricted likelihood function for an ARMA(<i>p</i>,<i>q</i>) model that can be used with a minimization program such as fminsearch.m. The ARMApqREMLfunct.m matlab program similarly gives the negative log likelihood function and restricted likelihood function for an ARMA(<i>p</i>,<i>q</i>) model for pseudo-ML and pseudo-REML estimation in which the standard error of the estimates is provided by the user. ARMApqREMLfunct_R.txt gives a version of ARMApqREMLfunct.m translated from matlab into R. The derivations of the code are given in Appendix A.
DOI: 10.6084/m9.figshare.3544517.v1
title: Supplement 1. MATLAB and R code for performing ARMA(p,q) model fitting.

description: File List ARMApqREMLfunct.m -- Matlab code for the ARMA likelihood function for REML and ML estimation ARMApq_ME_REMLfunct.m -- Matlab code for the ARMA likelihood function for pseudo-REML and pseudo_ML estimation ARMApqREMLfunct_R.txt -- R code for the ARMA likelihood function for REML and ML estimation Description The ARMApqREMLfunct.m matlab program gives the negative log likelihood function and restricted likelihood function for an ARMA(<i>p</i>,<i>q</i>) model that can be used with a minimization program such as fminsearch.m. The ARMApqREMLfunct.m matlab program similarly gives the negative log likelihood function and restricted likelihood function for an ARMA(<i>p</i>,<i>q</i>) model for pseudo-ML and pseudo-REML estimation in which the standard error of the estimates is provided by the user. ARMApqREMLfunct_R.txt gives a version of ARMApqREMLfunct.m translated from matlab into R. The derivations of the code are given in Appendix A.
DOI: 10.6084/m9.figshare.3544511
title: Appendix B. Details of the observational study.

description: Details of the observational study.
DOI: 10.6084/m9.figshare.3544508
title: Appendix C. ANOVA results of the experimental study.

description: ANOVA results of the experimental study.
DOI: 10.6084/m9.figshare.3544508.v1
title: Appendix C. ANOVA results of the experimental study.

description: ANOVA results of the experimental study.
DOI: 10.6084/m9.figshare.3544502
title: Appendix D. Detailed results from the observational study.

description: Detailed results from the observational study.
DOI: 10.6084/m9.figshare.3544502.v1
title: Appendix D. Detailed results from the observational study.

description: Detailed results from the observational study.
DOI: 10.6084/m9.figshare.3544499
title: Appendix A. Photographs of a representative vernal, autumnal, and permanent pond from the Mexican Cut Nature Preserve, Elk Mountains, Colorado, USA.

description: Photographs of a representative vernal, autumnal, and permanent pond from the Mexican Cut Nature Preserve, Elk Mountains, Colorado, USA.
DOI: 10.6084/m9.figshare.3544499.v1
title: Appendix A. Photographs of a representative vernal, autumnal, and permanent pond from the Mexican Cut Nature Preserve, Elk Mountains, Colorado, USA.

description: Photographs of a representative vernal, autumnal, and permanent pond from the Mexican Cut Nature Preserve, Elk Mountains, Colorado, USA.
DOI: 10.6084/m9.figshare.3544496
title: Appendix B. A table of results from MANOVA and univariate ANOVAs testing the effect of nonconsumptive Dytiscus beetle presence and caddisfly sex on size at emergence of Asynarchus caddisflies.

description: A table of results from MANOVA and univariate ANOVAs testing the effect of nonconsumptive Dytiscus beetle presence and caddisfly sex on size at emergence of Asynarchus caddisflies.