cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.13020/jt9r-tf03
title:  Light access and leaf trait variation within and among tree species across diverse mixtures within a common garden 

description: This dataset includes trait measurements for 2615 leaves of common temperate-boreal tree species alongside estimates of their light access. Trait values affect how plants function, with consequences that propagate through scales of ecological organization to affect ecosystem function. However, the pathway connecting trait expression to ecosystem function is complicated by feedbacks: trait expression may vary within species in response to community diversity, and trait expression also determines a community’s functional diversity. In this study, we quantify the extent to which light access – which past studies suggest affects trait expression and differs as a result of interactions among plants – differs consistently with community diversity and explains intraspecific trait variation in trees. In a common garden, trees of five angiosperm and seven gymnosperm species were planted to form 37 communities ranging widely in species and functional diversity whereby confounding environmental variation was minimized. We sampled leaves of each species to characterize intraspecific variation within crowns, among trees within communities, and among communities in three traits – leaf size, specific leaf area and nitrogen concentration – and estimated each leaf’s access to light.
description: Leaf trait measurements alongside estimates of light access for 2615 leaves from 12 common temperate-boreal tree species grown in diverse mixtures within a common garden.
DOI: 10.13020/jny1-wy60
title: R Code and Output Supporting: Computational reproducibility in The Wildlife Society's flagship journals

description: The goal of this study was to gauge the level of computational reproducibility, which is the ability to reach the same results using the same data and analysis methods, in the field of wildlife sciences. We randomly selected 80 papers published in the Journal of Wildlife Management and Wildlife Society Bulletin between 1 June 2016 and 1 June 2018. Of those for which we could obtain data, we attempted to reproduce their quantitative results using the original methods and data. The dataset shared in this repository is the de-identified results of our review, and the code provided here produces the results and figures in our published manuscript.
description: A full description of the data and code files is provided in the attached README.txt. Briefly, each html file uses the raw data (or processed data) to create results and figures for the manuscript. The script in 01_processing_data.html should be run first before any other subsequent scripts can be run. The zipped folder (item K) contains all of the Program R files (.R extension) for each of the html files.
DOI: 10.13020/nfr5-te36
title: Data for "The colloidal nature of complex fluids enhances bacterial motility"

description: Data appearing in the publication "The colloidal nature of complex fluids enhances bacterial motility". This paper reports the enhanced motion of bacteria in complex fluids. The archived data are the post-processed final data corresponding to figures in the manuscript as well as codes used for generating key plots.
DOI: 10.13020/d6w01v
title: Diverse bacterial communities exist on canine skin and are impacted by cohabitation and time

description: Dataset from sampling of 40 dogs over three time points. Dogs were paired across 20 households. Data is in raw fastq format from amplicon sequencing of the V1-V3 regions of the 16S rRNA gene using Illumina MiSeq.
description: This related study sampled 40 dogs from 20 households over the course of three seasons. Three skin sites were examined. The goal of the study was to determine if a core skin microbiome exists in dogs across time and body site, and if cohabitation impacts sharing of the skin microbiome. This dataset is a part of the Torres_Johnson Canine Microbiome Study.
description: Dataset from sampling of 40 dogs over three time points. Dogs were paired across 20 households. Data is in raw fastq format from amplicon sequencing of the V1-V3 regions of the 16S rRNA gene using Illumina MiSeq.
DOI: 10.13020/qy1k-8269
title: R code and data for "Survival of Sandhill Crane colts in Minnesota"

description: This collection of files provides data and R code supporting the publication "Survival of Sandhill Crane colts in Minnesota" currently in review at Journal of Fish and Wildlife Management. We provide all necessary data and code to reproduce the survival analysis of sandhill crane colts in Minnesota.
description: See ReadMe text file for a comprehensive description of all uploaded data files.
DOI: 10.13020/d69880
title: Fungal Endophytes as Priority Colonizers Initiating Wood Decomposition

description: Priority effects among wood decomposers have been demonstrated by manipulating fungal assembly history via inoculations in dead wood and then tracking community development using DNA sequencing. Individual wood-degrading fungi have been shown, however, to initiate decay after having colonized living trees as endophytes. To track these ‘upstream’ colonizers across the endophyte­saprophyte transition, we coupled high throughput sequencing with wood physiochemical analyses in stem sections extracted from healthy birch trees (Betula papyrifera; 4-7 cm dia.). We incubated wood in microcosms, limiting communities as endophytes­only or challenging endophytes with Fomes fomentarius or Piptoporus betulinus at high exogenous inoculum potential.  Initial fungal richness in birch stems averaged 143 OTUs, and decreased nearly three-fold after five months of decomposition. Although F. fomentarius successfully colonized some stem sections incubated at 25°C, decayed wood was generally dominated by saprophytic fungi that were present originally in lower abundances as endophytes.  Among saprophytes, fungi in the brown rot functional guild consistently dominated, matching wood residues bearing the chemical hallmarks of brown rot. Despite this functionally redundant outcome, the taxa that rose to dominate in individual sections varied. Surprisingly, the brown rot taxa dominating wood decomposition were better known for lumber degradation rather than log decay in ground contact.  Given the isolation from colonizers in our design, this redundancy of brown rot as the outcome suggests that these taxa and more generally brown rot fungi could have adapted to decompose wood where there is lower competitive pressure. Competitive avoidance would complement the diffuse depolymerization mechanisms of brown rot fungi, which are likely more prone to sugar pilfering by other organisms than the processive depolymerization mechanisms of white rot fungi.  Overall, this guild-level predictability of fungal endophyte development and consequence is encouraging given the challenges of predicting wood decomposition, and it provides a base for testing these dynamics under increasing natural complexity.
description: This repository contains the raw sequencing data for this study. The compressed file (Fungal_ITS1_MiSeq.zip) contains 82 illumia MiSeq 25 bp Read 1 FASTQ files. These files were used to generate the fungal community structure and function data in our paper, following the pipeline in the supplement File S1. The metadata of these samples were saved in the Excel file: Sample_metadata.csv
DOI: 10.13020/cwqe-ge69
title: Complete Data and Analysis for: Niche models differentiate potential impacts of two aquatic invasive plant species on native macrophytes

description: The goal of our study was to elucidate the mechanisms by which two invasive aquatic plant species (Myriophyllum spicatum and Potamogeton crispus) interact with native plant communities in lakes in Minnesota, USA. We used an observational dataset of aquatic plant occurrences—and associated light availability, depth, and temperature—to construct probabilistic models of the ecological niches of 34 aquatic plant species. We then compared shared-ness of these niches between the two invasive aquatic plants and 32 native species to infer the degree of direct competitive interaction. This repository contains the complete dataset as a comma-separated-value file and Program R code necessary to replicate the data prep, exploration, analysis, and visualizations presented in the manuscript.
description: The data file contains species identity, water depth, light availability at substrate, and growing degree days for 353,148 observations of aquatic plants in Minnesota, USA in the time period of 2001-2018. These data were compiled as described in the associated manuscript (https://doi.org/10.3390/d12040162). The Program R code will read in and summarize those data, construct niche models for a subset of the data and complete analyses needed to duplicate the results of the manuscript, and create visualizations used in publication.
DOI: 10.13020/89ae-2877
title: Horticultural availability and homeowner preferences drive plant diversity and composition in urban yards

description: Understanding the factors that influence biodiversity in urban areas is important for informing management efforts aimed at enhancing the ecosystem services in urban settings and curbing the spread of invasive introduced species. We determined the ecological and socioeconomic factors that influence patterns of plant richness, phylogenetic diversity and composition in 133 private household yards in the Minneapolis-Saint Paul Metropolitan area, Minnesota, USA. We compared the composition of spontaneously occurring plant species and those planted by homeowners with composition in natural areas (at the Cedar Creek Ecosystem Science Reserve) and in the horticulture pool of species available from commercial growers. Yard area and fertilizer frequency influenced species richness of the spontaneous species but expressed homeowner values did not. In contrast, the criteria that homeowners articulated as important in their management decisions—including aesthetics, wildlife, neatness and food provision—significantly predicted cultivated species richness. Strikingly, the composition of plant species that people cultivated in their yards resembled the taxonomic and phylogenetic composition of species available commercially. In contrast, the taxonomic and phylogenetic composition of spontaneous species showed high similarity to natural areas. The large fraction of introduced species that homeowners planted was a likely consequence of what was available for them to purchase. The study links the composition and diversity of yard flora to their natural and anthropogenic sources and sheds light on the human factors and values that influence the plant diversity in residential areas of a major urban system. Enhanced understanding of the influences of the sources of plants—both native and introduced—that enter urban systems and the human factors and values that influence their diversity is critical to identifying the levers to manage urban biodiversity and ecosystem services.
description: The files provide the plant species composition in 133 household yards in the Twin Cities including plants that are intentionally cultivated in yards and those that occur spontaneously. The native (N) and introduced (I) status of each species is given. Plant diversity metrics, calculated using a pruned phylogeny, are given for each yard, combined with survey responses of homeowners and other socioeconomic data.
DOI: 10.13020/zk0a-1e27
title: Validation of an automated shape-matching algorithm for biplane radiographic spine osteokinematics and radiostereometric analysis error quantification

description: Biplane radiography and associated shape-matching provides non-invasive, dynamic, 3D osteo- and arthrokinematic analysis. Due to the complexity of data acquisition, each system should be validated for the anatomy of interest. The purpose of this study was to assess our system’s acquisition methods and validate a custom, automated 2D/3D shape-matching algorithm relative to radiostereometric analysis (RSA) for the cervical and lumbar spine. Additionally, two sources of RSA error were examined via a Monte Carlo simulation: 1) static bead centroid identification and 2) dynamic bead tracking error. Tantalum beads were implanted into a cadaver for RSA and cervical and lumbar spine flexion and lateral bending were passively simulated. A bead centroid identification reliability analysis was performed and a vertebral validation block was used to determine bead tracking accuracy. Our system’s overall root mean square error (RMSE) for the cervical spine ranged between 0.21-0.49mm and 0.42-1.80º and the lumbar spine ranged between 0.35-1.17mm and 0.49-1.06º. The RMSE associated with RSA ranged between 0.14-0.69mm and 0.96-2.33º for bead centroid identification and 0.25-1.19mm and 1.69-4.06º for dynamic bead tracking. The results of this study demonstrate our system’s ability to accurately quantify segmental spine motion. Additionally, RSA errors should be considered when interpreting biplane validation results.
DOI: 10.13020/d6z597
title: R Code and Output Supporting: Do Capture and Survey Methods Influence Whether Marked Animals are Representative of Unmarked Animals?

description: These files contain R code (along with associated output from running the code) supporting all results reported in "Do Capture and Survey Methods Influence Whether Marked Animals are Representative of Unmarked Animals?" in Wildlife Society Bulletin.  The lead author wrote this code to analyze multi-year re-sighting data collected from moose (Alces alces) in Minnesota, elk (Cervus elaphus) in Washington, and mountain goats (Oreamnos americanus) in Washington and Alaska, to evaluate whether detection probabilities increased or decreased as a function of time since animals were captured.
description: The archive consists of 9 files:



1. WA_elk.R = R code used to analyze elk resighting data.

2. WA_elk.html = html output resulting from running the R code in WA_elk.R.  

3. Mtg_AK_WA.R = R code used to analyze mountain goat resighting data.  

4. Mtg_AK_WA.html = html output resulting from running the R code in Mtg_AK_WA.R.   

5. Moose_MN.R = R code used to analyze moose resighting data.  

6. Moose_MN.html = html output resulting from running the R code in Moose_MN.R.   

7. sightdat.csv = resighting data collected from moose in Minnesota between 2004 and 2007.

8. MTG_Sight_Alaska.csv = resighting data collected from mountain goats in Alaska.

9. NE_MN_Map.pdf = map of collection region for moose resighting data.
DOI: 10.13020/d6jx0p
title: Categorization of literature pertaining to the use of revegetation in suppressing invasive plant species

description: A search strategy was developed to identify literature on the use of revegetation as a strategy to suppress reinvasion of invasive species in grasslands and forests. This dataset summarizes the data points for each article included in the literature analysis.
DOI: 10.13020/femp-z102
title: Supporting data for 3D Printed Stem-Cell Derived Neural Progenitors Generate Spinal Cord Scaffolds

description: A bioengineered spinal cord is fabricated via extrusion-based multilateral 3D bioprinting, in which clusters of induced pluripotent stem cell (iPSC)-derived spinal neuronal progenitor cells (sNPCs) and oligodendrocyte progenitor cells (OPCs) are placed in precise positions within 3D printed biocompatible scaffolds during assembly. The location of a cluster of cells, of a single type or multiple types, is controlled using a point-dispensing printing method with a 200 μm center-to-center spacing within 150 μm wide channels. The bioprinted sNPCs differentiate and extend axons throughout microscale scaffold channels, and the activity of these neuronal networks is confirmed by physiological spontaneous calcium flux studies. Successful bioprinting of OPCs in combination with sNPCs demonstrates a multicellular neural tissue engineering approach, where the ability to direct the patterning and combination of transplanted neuronal and glial cells can be beneficial in rebuilding functional axonal connections across areas of central nervous system (CNS) tissue damage. This platform can be used to prepare novel biomimetic, hydrogel-based scaffolds modeling complex CNS tissue architecture in vitro and harnessed to develop new clinical approaches to treat neurological diseases, including spinal cord injury.
description: The ability to model CNS tissues in vitro for in vivo transplantation has the potential to be of critical importance in a variety of medical conditions such as spinal cord injury, traumatic brain injury, stroke, and degenerative neurologic disease. Our approach to generating functional CNS tissue constructs relies on a “multiprong” combination of sophisticated 3D bioprinting and cell culture expertise. Here, as an example for utilizing novel 3D neurobioprinting, we have devised a method to model the cytoarchitecture of spinal cord tissue.
DOI: 10.13020/rj08-sc66
title: Data supporting  Lung-to-ear sound transmission does not improve directional hearing in green treefrogs (Hyla cinerea)

description: Amphibians are unique among extant vertebrates in having middle ear cavities that are internally coupled to each other and to the lungs. In frogs, the lung-to-ear sound transmission pathway can influence the tympanum’s inherent directionality, but what role such effects might play in directional hearing remain unclear. In this study of the American green treefrog (Hyla cinerea), we tested the hypothesis that the lung-to-ear sound transmission pathway functions to improve directional hearing, particularly in the context of intraspecific sexual communication. Using laser vibrometry, we measured the tympanum’s vibration amplitude in females in response to a frequency modulated sweep presented from 12 sound incidence angles in azimuth. Tympanum directionality was determined across three states of lung inflation (inflated, deflated, reinflated) both for a single tympanum in the form of the vibration amplitude difference (VAD) and for binaural comparisons in the form of the interaural vibration amplitude difference (IVAD). The state of lung inflation had negligible effects (typically less than 0.5 dB) on both VADs and IVADs at frequencies emphasized in the advertisement calls produced by conspecific males (834 Hz and 2730 Hz). Directionality at the peak resonance frequency of the lungs (1558 Hz) was improved by ≅ 3 dB for a single tympanum when the lungs were inflated versus deflated, but IVADs were not impacted by the state of lung inflation. Based on these results, we reject the hypothesis that the lung-to-ear sound transmission pathway functions to improve directional hearing in frogs.
description: The 11 data files in this archive accompany the publication: Christensen-Dalsgaard J, Lee N, Bee MA (in press) Lung-to-ear sound transmission does not improve directional hearing in green treefrogs (Hyla cinerea). Journal of Experimental Biology.
DOI: 10.13020/d6qc7c
title: SOUND – System for Ultraconnected Network Degeneration (with code to analyze network geometrics)

description: This software models the economic mechanisms behind the decline of a surface transportation network, based on the assumption that the decline phase is a spontaneous process driven by decentralized decisions of individual travelers and privatized links. The software models a degeneration process by which the weakest link is removed iteratively from the network.
description: This is an applet that runs in Java, and the code and data files are included in a single zipped folder. To run the package, import the files as a project into Eclipse or another java platform. Run the main class, demo.java, as an applet.
DOI: 10.13020/03an-x606
title: Jacques Callot's Miseres de la guerre as narrative: 18 etchings from 1633

description: The etcher/engraver Jacques Callot printed the second state of Les Misères et malheurs de la guerre in 1633.  These images are in the public domain and the originals are held by Minneapolis Institute of Art. They are presented here in their entirety and in order, because viewing them together and as an ordered series shows that they form a narrative. It is being released now in advance of publication of my more extensive findings.
description: Additional information about these etchings can be found in the Minneapolis Institute of Art's online collection portal. The accession numbers for the etchings are consecutively ordered from P.1,357 for the title page to P.1,374 for image 18.
DOI: 10.13020/stas-pb42
title:  Wild rice geochemistry and reproductive life stage data from experimental pots amended with sulfate, 2016 

description: Wild rice, an annual aquatic plant produces fewer, smaller seeds with less nitrogen when exposed to sulfide, but does not produce decreased vegetative biomass. We compared the timing and duration of reproductive life stages in sulfate-amended plants to unamended plants to see how sulfide affects reproductive phenology. We recorded the life stage of plants starting with initiation of reproduction until senescence and measured seed count, mass and nitrogen content. Additionally, we sampled the geochemistry of porewater, sediment, and root surfaces to understand how plant life stage may control sediment redox conditions relevant to sulfide.
DOI: 10.13020/mx5w-vv32
title: Floral and leaf gas exchange and stem hydraulic conductance data observed from 2017 to 2018 on woody plants growing in Minnesota

description: These data were collected for a project examining floral water loss and floral hydration in woody plants that flower before they produce leaves. Gas exchange and stem hydraulic conductance were measured on at least six individuals of five woody species. These data were used to compare floral and leaf water loss and to evaluate whether floral water loss was limited by stem hydraulic conductance.
description: There are three CSV files and one readme file.
DOI: 10.13020/22bd-zk88
title: Winter oilseed pollinators in IA and MN in 2017 and 2018

description: Data include observations of insect pollinators visiting flowers of two winter oilseed crops (field pennycress and winter camelina) at three sites during the flowering seasons of  2017 and 2018. Two sites were in Minnesota and one site in Iowa each year.
The value of these data are that they document an important agroecosystem service provided by the two novel winter oilseed crops.
The purpose of saving the data files in the Digital Conservancy is to abide by new journal requirements that call for universal access to data used in professional qualifications.
description: Data include observations of insect pollinators visiting flowers of two winter oilseed crops (field pennycress and winter camelina) at three sites during the flowering seasons of  2017 and 2018. Two sites were in Minnesota and one site in Iowa each year.
DOI: 10.13020/d61s3s
title: Core 9 Biface Flake Models

description: This dataset consists of flake models representing an experimental archaeological reduction. This Core 9 Biface was knapped by Matthew D. Hunstiger. It and its related flakes are housed at the University of Minnesota's Department of Anthropology Evolutionary Anthropology Labs. These models are of the flakes that were created, or knapped off, as Hunstiger made that biface. They were created for the purpose of studying scar directionality in archaeological chipped stone analysis, and formed part of the experimental side of a dissertation by Matthew D. Hunstiger.
description: Dataset consists of one ZIP archive containing 25 virtual flake models, each represented by one OBJ file with an accompanying MTL file, for 50 total files. The flakes were scanned with a NextEngine Inc.’s Desktop 3D Scanner SD (standard definition) or HD (high definition), and then virtually assembled using 3D Systems' Inc. Geomagic Design X and Verify. These models can be viewed with a variety of software, for example http://3dviewer.net/.