cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.13020/d6w30h
title: Core 3 Biface Flake Models

description: This dataset consists of flake models representing an experimental archaeological reduction. This Core 3 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 18 virtual flake models, each represented by one OBJ file with an accompanying MTL file, for 36 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/.
DOI: 10.13020/d68q38
title: Data from "Detrimental effects of rhizobial inoculum early in the life of the partridge pea Chamaecrista fasciculata"

description: Premise of the study: Mutualistic relationships with microbes may aid plants in overcoming environmental stressors, and increase the range of abiotic environments where plants can persist. Rhizobia, nitrogen-fixing bacteria associated with legumes, often confer fitness benefits to their host plants by increasing access to nitrogen in nitrogen-limited soils, but effects of rhizobia on host fitness under other stresses, such as drought, remain unclear.

Methods: In this greenhouse study, we varied application of rhizobia (Bradyrhizobium sp.) inoculum and drought to examine whether the fitness benefits of rhizobia to their host, the partridge pea (Chamaecrista fasciculata), would differ between drought and well-watered conditions. Plants were harvested nine weeks after seeds were sown.

Key results: Young Chamaecrista fasciculata plants that had been inoculated had lower biomass, leaf relative growth rate, and stem relative growth rate compared to young uninoculated plants in both drought and well-watered environments. 

Conclusions: Under the conditions of this study, the rhizobial inoculation imposed a net cost to their hosts early in development. Potential reasons for this cost include allocating more carbon to nodule and root development than to above-ground growth and a geographic mismatch between the source populations of host plants and rhizobia. If developing plants incur such costs from rhizobia in nature, they may suffer an early disadvantage relative to other plants, whether conspecifics lacking rhizobia or heterospecifics.
description: These data files include data on relative growth rate, biomass, and soil moisture from Pain et al. 2018 (American Journal of Botany). See readme file associated with each data file for more information.
DOI: 10.13020/pz48-e352
title:  Terrestrial gastropod collection data taken during an experiment co-grazing goats with waterfowl at UMN's Rosemount Research and Outreach Center 

description: The data describe terrestrial gastropod sampling from an experiment examining whether co-grazing goats with waterfowl can reduce the number of intermediate hosts of a potentially deadly parasite, Parelaphostrongylus tenuis. Data were collected during two years and at two timepoints at UMN's Rosemount Research and Outreach Center, specifically in Lone Rock Woods. Data may be useful for others doing an inventory of terrestrial gastropod species in Minnesota. It is being released in conjunction with a manuscript currently in revision with EcoHealth.
description: A csv data file and a readme file with meta-data.
DOI: 10.13020/qfwg-tn13
title: Data Related to Meta-analysis of up to 622,409 individuals identifies 40 novel smoking behaviour associated genetic loci

description: Smoking is a major heritable and modifiable risk factor for many diseases, including cancer, common respiratory disorders and cardiovascular diseases. We tested up to 235,116 single nucleotide variants (SNVs) on the exome-array for association with smoking initiation, cigarettes per day, pack-years, and smoking cessation in a fixed effects meta-analysis of up to 61 studies (up to 346,813 participants). SNV-trait associations with P < 5 × 10−8 in either analysis were taken forward for replication in up to 275,596 independent participants from UK Biobank. Lastly, a meta-analysis of the discovery and replication studies was performed. These novel loci will facilitate understanding the genetic aetiology of smoking behaviour and may lead to the identification of potential drug targets for smoking prevention and/or cessation.
description: Here we have included four sets of meta-analysis results: Meta-analysis of discovery and replication cohorts, combining genotyped Exome-chip and Axiom array content for (i) Smoking Initiation, (ii) Cigarettes per day, and (iii) Smoking Cessation, and (iv) meta-analysis of discovery cohorts for Pack Years.
DOI: 10.13020/6qrp-wy09
title: Video Diver Dataset (VDD-C), 100,000 annotated images of divers underwater

description: This dataset contains over 100,000 annotated images of divers underwater, gathered from videos of divers in pools and the Caribbean off the coast of Barbados. It is intended for the development and testing of diver detection algorithms for use in autonomous underwater vehicles (AUVs). Because the images are sourced from videos, they are largely sequential, meaning that temporally aware algorithms (video object detectors) can be trained and tested on this data. Training on this data improved our current diver detection algorithms significantly because we increased our training set size by 17 times compared to our previous best dataset.  It is released for free for anyone who wants to use it.
description: The data of VDDC comes in four zip files:
- original_data.zip: Contains the original images and .xml label files, along with some information required to process the data into the proper formats. 
- script.zip: Contains the script used to generate the labels and images folders from the original_data. 
- labels.zip: Contains a variety of label types, in voc, yolo, tfrecord, and tfsequence formats. These labels are also properly filtered to correct inaccurate coordinates for annotations and remove unwanted annotations. 
- images.zip: Contains the images of the dataset, filtered to remove poor quality images.
DOI: 10.13020/d6zp4h
title: Frogs Exploit Statistical Regularities in Noisy Acoustic Scenes to Solve Cocktail-Party-Like Problems

description: This submission is a supplement to the paper entitled “ Frogs Exploit Statistical Regularities in Noisy Acoustic Scenes to Solve Cocktail-Party-Like Problems” by Lee et al. (2017) published in Current Biology. In this paper, we develop an auditory filterbank inspired by the frog peripheral auditory system to quantify the natural scene statistics of frog breeding choruses. We show that natural chorus noise exhibits a high-level of spectrotemporal correlation (comodulation) among frequencies emphasized in advertisement calls. In 4 psychophysical experiments, we demonstrate that treefrogs can exploit comodulation in background noise to mitigate noise-induced errors in evolutionary critical mate-choice decisions.Frogs experienced fewer errors in recognizing conspecific calls and in selecting calls of high-quality mates in the presence of comodulated noise. This submission includes
 an implementation of the frog auditory filterbank in Matlab, source data, and other Matlab code used in data analyses to generate the main and supplemental figures presented in Lee et al. (2017).
description: This submission is a supplement to the paper entitled “ Frogs Exploit Statistical Regularities in Noisy Acoustic Scenes to Solve Cocktail-Party-Like Problems” by Lee et al. (2017) published in Current Biology. In this paper, we develop an auditory filterbank inspired by the frog peripheral auditory system to quantify the natural scene statistics of frog breeding choruses. We show that natural chorus noise exhibits a high-level of spectrotemporal correlation (comodulation) among frequencies emphasized in advertisement calls. In 4 psychophysical experiments, we demonstrate that treefrogs can exploit comodulation in background noise to mitigate noise-induced errors in evolutionary critical mate-choice decisions.Frogs experienced fewer errors in recognizing conspecific calls and in selecting calls of high-quality mates in the presence of comodulated noise. This submission includes
an implementation of the frog auditory filterbank in Matlab, source data, and other Matlab code used in data analyses to generate the main and supplemental figures presented in Lee et al. (2017).
DOI: 10.13020/d6vq25
title: ableC: Extensible Specification of C Using the Silver Attribute Grammar System

description: This is the Silver specification of ableC: a specification of C at the ISO C11 standard. There may be newer, unarchived versions of this software at http://melt.cs.umn.edu.
DOI: 10.13020/d6jm43
title: Link Lists for Websites Reporting Information on Hurricane Sandy from 2003 to 2012

description: Data contains hyperlinks that existed between websites reporting information on Superstorm Sandy from 2003 – 2012. The data tracks 20,013,455 unique URLs.
description: Data are structured in a standard link list format, including source, destination, frequency and any associated descriptive text. See the readme file for more detailed information.
DOI: 10.13020/j01t-wq81
title: Springer Lab UAV Maize Phenotyping Project at UMN StPaul: 2018 and 2019

description: This dataset provides a valuable resource for evaluating the utility of unmanned aerial vehicles to collect phenotypic data in agricultural fields. Many flights throughout the growing season of a maize experiment were conducted and this dataset includes digital elevation models generated from images within these flights, the plot boundary shapefiles for plot identification, plant height values extracted following Tirado et al., 2019 procedure, hand measurement height values conducted following flights, and yield data for each plot. This maize experiment consisted of twelve hybrids planted at three different planting densities (low, medium and high) and two planting dates (early and late) across two years and therefore provides a valuable resource for evaluating how temporal data collected from UAVs can aid in assessing plant productivity. It can also be utilized to develop and test different protocols for plant height extraction from DEMs at different growth stages as the hand measurements can be used to test the accuracy.
description: Files include digital elevation models for all flights of our maize field in the summer of 2018 and 2019, the plot boundary shapefiles, information on each plot including planting date and density and stand counts, yield data for all plots, and weather station data for both summers.  More detailed info can be found in the readme file.
DOI: 10.13020/d6t88n
title: Three-Dimensional Models of Experimentally-Produced Lithic Artifacts Created using an Expedient and Refined Photogrammetry Protocol

description: The data set consists of three-dimensional (3D) models of experimentally produced lithic artifacts created using both expedient and refined photogrammetric setups and processing protocols. Source images for all models were captured using a 12.1 megapixel Canon PowerShot SX260 HS compact digital camera. In our expedient protocol, objects were placed on a wire stand. The photographer moved around the object, and captured photos using Auto mode. In our refined protocol, objects were placed on a rotating turntable under controlled lighting conditions. The camera was placed on a tripod. Shutter speed, f-stop, and ISO were set manually. This refined protocol is described in Porter, S. T., Roussel, M., & Soressi, M. (2016). A Simple Photogrammetry Rig for the Reliable Creation of 3D Artifact Models in the Field Lithic Examples from the Early Upper Paleolithic Sequence of Les Cottés (France). Advances in Archaeological Practice, 4(1), 71-86. The associated paper discusses the relative fidelity of the models produced using these different workflows. Models may also be viewed online (in browser) at: https://sketchfab.com/unlarchaeology/collections/magnani-et-al-2016.
description: The data are divided into four ZIP files based on whether they contain core or flake models, and whether the models were created using an expedient or refined photogrammetric setup and protocol. Each of these .ZIP files contains the relevant 3D models in OBJ format. There are three files associated with each model (OBJ, MTL, and JPG texture). The files are named based on object ID, and the setup used to create them (i.e. expedient or refined). All models were processed and scaled in Agisoft PhotoScan Professional Edition. Geomagic Design X was used to center and align models around the origin.
DOI: 10.13020/d6qg61
title: Epidermal Growth Factor Receptor Signaling Mediates the Proinflammatory Effects of Staphylococcus aureus Gamma Toxin on the Mucosa

description: The data are the experimental data used to generate figures for the paper entitled "Epidermal Growth Factor Receptor Signaling Mediates the Proinflammatory Effects of Staphylococcus aureus Gamma Toxin on the Mucosa". The data are being released to comply with PloSONE data availability policy.
description: Methods for data collection are included in the upload.
DOI: 10.13020/dygy-qx38
title: EEG data for 2 experiments related to Auditory Enhancement
DOI: 10.13020/d6w89n
title: Supporting Data for “Engineering of a Highly Efficient Escherichia coli Strain for Mevalonate Fermentation through Chromosomal Integration”

description: These files contain data along with associated output from instrumentation supporting all results reported in Wang, J.; Niyompanich, S.; Tai, Y.-S.; Wang, J.; Bai, W.; Mahida, P.; Gao, T.; Zhang, K. Engineering of a highly efficient escherichia coli strain for mevalonate fermentation through chromosomal integration. Appl. Environ. Microbiol., 2016, 82, 7176–7184. Chromosomal integration of heterologous metabolic pathways is optimal for industrially relevant fermentation, as plasmid-based fermentation causes extra metabolic burden and genetic instabilities. In this work, chromosomal integration was adapted for the production of mevalonate, which can be readily converted into β-methyl-δ-valerolactone, a monomer for the production of mechanically tunable polyesters. The mevalonate pathway, driven by a constitutive promoter, was integrated into the chromosome of Escherichia coli to replace the native fermentation gene adhE or ldhA. The engineered strains (CMEV-1 and CMEV-2) did not require inducer or antibiotic and showed slightly higher maximal productivities (0.38 to ∼0.43 g/liter/h) and yields (67.8 to ∼71.4% of the maximum theoretical yield) than those of the plasmid-based fermentation. Since the glycolysis pathway is the first module for mevalonate synthesis, atpFH deletion was employed to improve the glycolytic rate and the production rate of mevalonate. Shake flask fermentation results showed that the deletion of atpFH in CMEV-1 resulted in a 2.1-fold increase in the maximum productivity. Furthermore, enhancement of the downstream pathway by integrating two copies of the mevalonate pathway genes into the chromosome further improved the mevalonate yield. Finally, our fed-batch fermentation showed that, with deletion of the atpFH and sucA genes and integration of two copies of the mevalonate pathway genes into the chromosome, the engineered strain CMEV-7 exhibited both high maximal productivity (∼1.01 g/liter/h) and high yield (86.1% of the maximum theoretical yield, 30 g/liter mevalonate from 61 g/liter glucose after 48 h in a shake flask).
description: Full description in the file "WangReadme.rtf". 

The files below includes the pathway design (Fig. 1) and the bioengineering experimental data. Figure numbers in associated paper also include raw experimental data. The concentrations of feedstock (glucose), intermediate (acetate and pyruvate), and product (mevalonate) were measured by high-performance liquid chromatography (HPLC). The dataset includes one ChemDraw (.cdx) file. CDX files can be opened with proprietary ChemDraw 12.0, distributed by CambridgeSoft.
DOI: 10.13020/598v-vr53
title: Parole Rules in the United States: Conditions of Parole in Historical Perspective, 1956-2020

description: Data set of six censuses of standard conditions of parole that have been conducted between 1956 and 2020
description: Data set of six censuses of standard conditions of parole that have been conducted between 1956 and 2020.
description: This data set contains qualitatively coded standard conditions of parole for each jurisdiction of the United States of America for roughly every twelve years from 1956 to 2020. There are ten .csv files: five files of parole rules censuses spanning 1956 to 2008, compiled by previous researchers in the past and coded by the authors; a census of parole rules for 2020, compiled and coded by the authors; a category count by census year; a condition count by census year and jurisdiction; a category cross-walking chart for the six censuses; and a raw text coding matrix for the 2020 census. There is also a .txt Readme file.
DOI: 10.13020/d6x30t
title: Dibble Levallois Flake Models

description: This dataset consists of flake models representing an experimental archaeological reduction. This Dibble Levallois reduction was knapped by Harold L. Dibble. It and its related flakes are housed at the University of Arizona's School of Anthropology. These models are of the flakes that were created, or knapped off, as Dibble made that levallois reduction. 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 34 virtual flake models, each represented by one OBJ file with an accompanying MTL file, for 68 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/.
DOI: 10.13020/9wb9-kj10
title:  Wind turbine wake flow visualization data from experiments conducted at UMore park on March 5-6, 2018 and April 8-9, 2018 

description: This data includes flow visualization videos using natural snowfall in the wake of a utility-scale (2.5 MW) wind turbine. In addition, the meteorological and SCADA data from the same time periods are included. These datasets are used to analyze the interaction between the wind turbine wake and the ground surface, which has important implications for understanding the impact of wind farms on their surroundings, particularly in the area of agriculture.
description: Meteorological data and SCADA data from the two experiments, video data from the two experiments, experiment logs from the two experiments
DOI: 10.13020/d6hq22
title: Mind the Gap: the evolution of oviposition site and specialisation in the parasitoid superfamily Chalcidoidea

description: Parasitoid wasps have contributed significantly to our understanding of ecological specialisation and the evolution of traits linked to host range. Oviposition site is one such trait. Endoparasitoids deposit their eggs inside the host body and tend to be more highly specialised than ectoparasitoids (which lay eggs externally) because they must develop specific strategies to overcome host immune defences. Intermediate to endo- and ectoparasitism is a strategy that we call ‘gap laying’. Gap-laying parasitoids deposit their eggs between the hard outer puparium and the larva of dipteran hosts. This behaviour has received less empirical attention than endo- and ectoparasitism but has important implications for the evolution of specialisation. Using a phylogenetically controlled comparative approach we find that gap-laying species in the hymenopteran superfamily Chalcidoidea exhibit numeric host ranges intermediate to endo- and ectoparasitoids, but these groups exploit a similarly taxonomically related range of hosts. We found that gap-laying can arise from ectoparasitism or endoparasitism, but once it evolves it shows patterns consistent with an evolutionary dead-end compared to other strategies. The results of this study demonstrate how oviposition site, beyond the normal endo-ectoparasitoid dichotomy, influences host specificity, shedding light on the causes and consequences of ecological specialisation in the parasitic Hymenoptera.
description: Trait files for all species and traits, newick file for composite phylogeny, spreadsheet containing frequencies of all transitions across all most parsimonious reconstructions.
DOI: 10.13020/kxm7-vp82
title: Data for: A Review of Literature Published in EMIP from 2005-2019

description: Within any scientific field, there is an occasional need to summarize existing research—to not only reflect on current thinking, but to also indicate where the field may be headed. This holds particularly true in the field of educational measurement, where, to date, there has not been a review of general measurement practices in the published literature. To fill this gap, this study conducted a review investigating the author, keyword, methodological, and citation characteristics of empirical studies published in Educational Measurement: Issues and Practice from 2005-2019.

Included are the data for the study, keyword, and citation analysis, as well as the code used to conduct these analyses.
DOI: 10.13020/d6fd43
title: EBSD data for sheared partially molten rocks (olivine + basalt)

description: This data set contains the EBSD data for samples of olivine + basaltic melt deformed in torsion. The results are published in "Crystallographic preferred orientation of olivine in sheared partially molten rocks: The source of the 'a-c switch'" by Chao Qi, Lars Hansen, David Wallis, Ben Holtzman and David Kohlstedt on Geochemistry, Geophysics, Geosystems (G-cubed) 2018.
description: The samples included in this data set are 0609, 0705, 0765, 0767, 0775, 0817. 
Files are .ctf files exported from the HKL channel5 software. Basic noise reduction has been done as described in the paper.  
Each file is named by the sample number and the section of the map.
DOI: 10.13020/4gms-4q97
title: Supporting Data for Internal Structure of Methylcellulose Fibrils

description: Data files used to generate all figures in the manuscript "Internal Structure of Methylcellulose Fibrils" and its supplementary information.
DOI: 10.13020/d65x1n
title: Link Lists for Websites of the US House of Representatives in 2009

description: Data contains hyperlinks that existed between websites that were part of the United States House of Representatives domain in 2009. The data track 12,410,014 unique URLs.
description: Data are structured in a standard link list format, including source, destination, frequency and any associated descriptive text. See the readme file for more detailed information.
DOI: 10.13020/mae6-4t39
title: Marcell Experimental Forest Black Spruce Dendrochronology

description: This data set includes raw tree ring width files of black spruce trees collected from six peatlands at the Marcell Experimental Forest. The data were collected for the purpose of investigating the roles of peatland water table elevations on black spruce growth.