cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.13020/d6xm2r
title: Nonlinear Processing of a Multicomponent Communication Signal by Combination‑Sensitive Neurons in the Anuran Inferior Colliculus

description: This submission is a supplement to the paper entitled "Nonlinear processing of a multicomponent communication signal by combination-sensitive neurons in the anuran inferior colliculus" by Lee et al. (2017) published in the Journal of Comparative Physiology A. We investigated how female green treefrogs (Hyla cinerea) integrate multiple spectral components present in male advertisement calls. Typical calls have a bimodal spectrum consisting of low-frequency (0.9 kHz) and high-frequency (2.7 kHz) components that are transduced by different sensory organs in the inner ear. In behavioral experiments, only bimodal calls reliably elicited phonotaxis in no-choice tests, and they were selectively chosen over unimodal calls in two-alternative choice experiments. Single-unit recordings from the inferior colliculus of awake, passively listening subjects were classified as combination-insensitive (27.9%) or combination-sensitive units (72.1%) based on patterns of relative responses to the same bimodal and unimodal calls. Combination-insensitive units responded similarly to the bimodal call and one or both unimodal calls. In contrast, combination-sensitive units exhibited both linear responses and, more commonly, nonlinear responses to the spectral combination in the bimodal calls. Nonlinearities play potentially critical roles in spectral integration and in the neural processing of multicomponent communication signals. This submission includes source data used in generating the figures presented in the paper.
DOI: 10.13020/d6hs34
title: Core 12 Discoidal Flake Models

description: This dataset consists of flake models representing an experimental archaeological reduction. This Core 12 Discoidal 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 discoidal 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: This dataset consists of flake models representing an experimental archaeological reduction. This Core 12 Discoidal reduction 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 discoidal 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 31 virtual flake models, each represented by one OBJ file with an accompanying MTL file, for 62 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: 10.13020/0f8c-k469
title:  VCF file of SNP data of 556 isolates of the wheat leaf rust fungus, Puccinia triticina from 11 world-wide regions

description: This a file of ca. 6500 SNPs of 556 isolates of the wheat leaf rust fungus, Puccina triticina from 11 worldwide regions that were mapped to the reference genome. This data was used to examine the population structure of Puccinia triticina on a worldwide basis, and to examine the evolutionary relationship between collections from a wheat progenitor, collections from durum wheat, and collections from common wheat. Groups of isolates that were highly related were found in distant continental regions, indicating past and current migration of this important wheat pathogen. Data is being released now in conjunction with publication of a primary research paper that describes this research. The second file give the virulence/virulence of the same isolates to 20 lines of Thatcher wheat that differ for single leaf rust resistance genes.
description: This dataset includes SNPs of 556 isolates of the wheat leaf rust fungus, Puccina triticina from 11 worldwide regions that were mapped to the reference genome. This data was used to examine the population structure of Puccinia triticina on a worldwide basis, and to examine the evolutionary relationship between collections from a wheat progenitor, collections from durum wheat, and collections from common wheat. Groups of isolates that were highly related were found in distant continental regions, indicating past and current migration of this important wheat pathogen. Data is being released now in conjunction with publication of a primary research paper that describes this research.
description: We provide variant calls in VCF and fasta format. Fasta formatted data were used with the deposited python script to calculate the average number of pairwise differences between sequences. GBS SNP calls in Variant Call Format (bgzipped) GBS Haplotype sequence in fasta format (tarballed directory) Python script for calculating average number of pairwise differences using the fasta haplotypes as input. Names dependency file for python script. The excel file gives the virulence/virulence of the same isolates to 20 lines of Thatcher wheat that differ for single leaf rust resistance genes.
DOI: 10.13020/m02h-nq46
title:  Sample and genetic data: Muskellunge (Esox masquinongy) movement patterns and habitat use in the St. Louis River Estuary and southwestern Lake Superior 

description: Sample data and microsatellite genotypes for 258 muskellunge, including 60 with acoustic tags, collected in 2017 from the St. Louis River estuary of Lake Superior. Genetic data were used to assign strain ancestry from two stocked sources (from Minnesota and Wisconsin). Ancestry, sex and length were used as variables when examining movement patterns using an acoustic receiver array in the estuary and Lake Superior.
description: Sample data and microsatellite genotypes for 258 muskellunge, including 60 with acoustic tags, from the St. Louis River estuary of Lake Superior in a CSV spreadsheet file. Data include length, sex, strain classification and allele scores for 13 microsatellite loci.
DOI: 10.13020/d63s3d
title: 2011 Rock Properties Database: Density, Magnetic Susceptibility, and Natural Remanent Magnetization of Rocks in Minnesota

description: Geologic interpretation of gravity and magnetic anomaly data in a given area is greatly enhanced if

density, magnetic susceptibility (MS) and natural remanent magnetization (NRM) data are available for

representative rock-types (Chandler and others, 2008). Along with geologic information from outcrop

and drill-holes, rock property data help relate geophysical anomaly signatures to probable rock types,

and provide constraints on the use of anomaly data as a tool for mapping and for modeling geology at

depth. Rock property data are particularly important to Minnesota where Precambrian rocks, which

comprise the bulk of the bedrock surface, are associated with a wide range of density, MS and NRM

values and are mostly under a thick cover of unconsolidated glacial sediments.
description: The current database consists of location 9,032 entries. The surface-based, point data include

5,272, 6,939, and 903 density, magnetic susceptibility, and NRM measurements, respectively. Downhole

data from 146 drillcore have also been incorporated, yielding an additional 1,145 and 9,622

measurements of density and magnetic susceptibility, respectively. Finally, the location of new and

some pre-existing rock property sites was improved by using outcrop polygons and improved base-map

overlays to adjust point locations to most-likely positions as necessary. Thus, the revised database

represents a significant improvement in size, types of material, and quality, and should serve the needs

of the MGS and the broader geologic community for many years to come. The thumbnail was taken from a figure in the report that shows the point locations in the 2011 rock property database superimposed on the 2011 bedrock geology map of Minnesota.
DOI: 10.13020/d64x2q
title: Data, Model Documentation, and Output Supporting "Optimizing syndromic health surveillance in free ranging great apes: the case of Gombe National Park"

description: Syndromic surveillance is an incipient approach to early wildlife disease detection. Consequently, systematic assessments are needed for methodology validation in wildlife populations. We evaluated the sensitivity of a syndromic surveillance protocol for respiratory disease detection among chimpanzees in Gombe National Park, Tanzania. Empirical health, behavioral and demographic data were integrated with an agent-based, network model to simulate disease transmission and surveillance. Surveillance sensitivity was estimated as 66% (95% Confidence Interval: 63.1, 68.8%) and 59.5% (95% Confidence Interval: 56.5%, 62.4%) for two monitoring methods (weekly count and prevalence thresholds, respectively), but differences among calendar quarters in outbreak size and surveillance sensitivity suggest seasonal effects. We determined that a threshold weekly detection of ≥2 chimpanzees with clinical respiratory disease leading to outbreak response protocols (enhanced observation and biological sampling) is an optimal algorithm for outbreak detection in this population. 

Synthesis and applications: This is the first quantitative assessment of syndromic surveillance in wildlife, providing a model approach addressing disease emergence. Coupling syndromic surveillance with targeted diagnostic sampling in the midst of suspected outbreaks will provide a powerful system for detecting disease transmission and understanding population impacts.
description: Data files include documentation of a disease simulation model, simulation data produced from the model, as well as input data used to parameterize the model.
DOI: 10.13020/s2jm-1j25
title: Adverse Childhood Experiences: A Scoping Review of Measures and Methods I: Definitions, Publication Trends, Study Purposes, Funding Sources, Country of the Samples, and Study Sources

description: The items included in this depository are the materials needed to replicate the methodology and results of the first paper based on a scoping review of research on adverse childhood experiences (ACEs).
description: The file "rayyan articles" is a spreadsheet of all the articles that were screened to determine whether they were eligible for the literature review. The file includes the decisions to include or exclude as well as reasons for inclusion. The file "Consensus data for the ACEs lit review_Paper 1" contains the consensus decisions on the set of variables included in the first paper. The "Lit_reviewR" file contains the same data in a CSV format, and is read in to the R script used for data analysis, "Data_analyses_ACEs_lit_review_Paper1.R". The "Journals" file contains a list of all the journals the eligible articles were published in . We also uploaded the Method section of the paper, which is necessary for replicating the study. The study was conducted in Minnesota, and all co-authors are affiliated with the University of Minnesota.
DOI: 10.13020/rhbq-rc90
title:  Soybean Aphid and Aphelinus certus Development (2017–2019) 

description: These data detail the results of four laboratory bioassays involving soybean aphid and Aphelinus certus: aphid development, no-choice parasitoid development, host-stage preference, and post-parasitism reproduction. Data related to density-dependent adult parasitoid lifespan are also included. Metadata are included in each file.
DOI: 10.13020/5bdw-8r09
title: Wigner-Seitz Cell generation and calculations in MATLAB

description: This series of MATLAB codes was developed to generate publication-quality Wigner-Seitz cells for a variety of structures. These are frequently desired for self-assembled micellar systems, wherein the geometry of the Wigner-Seitz cell plays a role in the emergence of several packings. The main algorithm (VoronoiTesselation.m) is generalized, allowing specification of lattice positions and parameters or the upload of these values from a .xtl file exported from Vesta. Added is the ability to determine various cell parameters, including the coordination number, area/volume, and the second-moment volume, which is proportional to the stretching moment for polymer chains stretched from the cell center to the cell edges. A simple algorithm for simulation of 2D diffraction patterns is also included (diffraction.m).
description: Voronoi (Wigner-Seitz) cells and related calculations can be performed using VoronoiTesselation.m. The code is heavily commented with instructions included. Sample .xtl structure files exported from Vesta are included for various crystals and are readily loaded into the program.

2D diffraction patterns can be simulated using the associated diffraction.m script. The angle of the structure relative to an incident beam is readily changed and various structures can be examined using the same structure loading algorithms used for VoronoiTesselation.m.  See link to index 1D SAXS data: https://hdl.handle.net/11299/223278
DOI: 10.13020/d6h596
title: "Laundry Soap" from the Ojibwe Conversations Archives Project

description: Two first speakers of Ojibwe discuss and debate laundry soap in a video recorded in Hayward WI in March 2009.
description: These data files include the primary video, an audio file, and a transcript of the video created using ELAN software to track the words and timestamps of the audio track. The transcription software files are included in the zipped folder called "Annotated Video Files." The transcription is translated from Ojibwe to English and is presented as a pdf file.
DOI: 10.13020/d64g6r
title: Environmental Association Analyses Identify Candidates for Abiotic Stress Tolerance in Glycine soja, the Wild Progenitor of Cultivated Soybeans

description: Understanding the genetics basis of adaption is a fundamental goal of biological research. The present study explores an ex situ conservation collection, the USDA germplasm collection, genotyped at 32,416 SNPs, to identify population structure and test for associations with bioclimatic and biophysical variables in Glycine soja, the wild progenitor of Glycine max (soybean). Candidate loci were detected that putatively contribute to adaptation to abiotic stresses.
description: The sampled accessions in this study are derived from the SNPs genotyped by Song et al. (2015) and catalogued in the USDA soybean germplasm collection (http://soybase.org/snps/index.php). Accessions without latitudinal and longitudinal data were excluded, as were those with greater than 10% of data missing. Additionally, eight accessions from Taiwan and Northern Russia were excluded due to those being geographical outliers. A list of accessions used in the study can be found in the data files below. Environmental association was performed using data from public repositories of global bioclimatic (WorldClim) and biophysical variables (ISRIC), and a list of the variables retrieved per accession can be found in the data files below.
DOI: 10.13020/d6m66b
title: Photochemical Data of Stormflow Samples Collected Near Minneapolis and St. Paul, Minnesota from 2014-September to 2015-October

description: Stormflow samples were collected from 31 sites near Minneapolis and St. Paul, Minnesota between 2014-September and 2015-October. Optical and photochemical parameters of the samples were measured under controlled laboratory conditions. The data were collected to better understand the way in which land cover with variable levels of human impact influence the formation rate and yield of triplet excited states of dissolved natural organic matter (3DOM*). Rates of formation (Rf,T) and apparent quantum yields (AQYT) were measured for 3DOM* using the chemical probe, 2,4,6-trimethylphenol, under a broadband xenon-arc lamp with a 290-nm wavelength filter.
DOI: 10.13020/d6f30g
title: MATLAB code for "Fast In-Plane Dynamics of a Beam with Unilateral Constraints"

description: A computationally efficient technique to simulate the dynamic response of a beam colliding with rigid obstacles is described in this paper. The proposed method merges three key concepts. First, a low order discretization scheme that maximizes the number of nodes of the discrete model, where impacts are detected, at the expense of the degree of continuity of the constructed displacement field. Second, the constrained problem is transformed into an unconstrained one by formulating the impact by means of a complementarity Signorini's law involving the impulse generated by the collision and the pre- and post- impact velocity linked via a coefficient of restitution. Third, Moreau's midpoint time-stepping scheme developed within the context of colliding rigid bodies, is used to advance the solution.
description: These MATLAB codes demonstrate the method proposed by the paper of the same name. HeMo evaluates the dynamic response of a cantilever beam against two symmetrical stops ((end)-point and/or horizontal wall). The  impact motion is simulated by two methods: a)  Moreau's midpoint method and b)  Moreau-Jean's theta method. The second code, Rayleigh, measures the response of a Rayleigh beam for unit impulse load with beta=0.1 (Fourier series - 6 modes).
DOI: 10.13020/f50r-zh70
title: Airborne methane measurements from the GEM study: Facility-level sampling

description: This archive contains airborne measurements from the GEM campaign. Data are archived in association with the following manuscript: Yu, X., D.B. Millet, K.C. Wells, T.J. Griffis, X. Chen, J.M. Baker,
S.A. Conley, M.L. Smith, A. Gvakharia, E.A. Kort, G. Plant, and J.D. Wood (2020), Top-down constraints on methane point source emissions from animal agriculture and waste based on new airborne measurements in the US Upper Midwest, J. Geophys. Res., 125, e2019JG005429, doi:10.1029/2019JG005429.
description: Please see README file for a detailed description of the data.
DOI: 10.13020/wn56-9y75
title: R Code and Output Supporting:  Resampling-Based Methods for Biologists

description: This repository contains data, R code, and associated output from running R code supporting results reported in:
 
Fieberg, J., K. Vitense, and D. H. Johnson 2020. Resampling-Based Methods for Biologists. PeerJ [In Revision]
description: See readme file.
DOI: 10.6069/187r-x165
title: Puget Sound Stormwater Utility Fee and Stormwater Program Budget Dataset
DOI: 10.5063/f1k9360f
title: The Sacramento-San Joaquin Delta genus and community level classification maps derived from airborne spectroscopy data

description: Since 2004, airborne hyperspectral imagery has been acquired over the Sacramento - San Joaquin Delta in northern California to map submerged and floating invasive species and study how they affect the Delta ecosystem. Acquiring imagery over 2220 square kilometers of the Delta typically required 60-70 flightlines each year, which were then further processed to surface reflectance, georegistered, and prepared for analysis. Further, each flightline was processed using multiple spectral mapping methods such as spectral angle mapper, spectral mixture analysis, spectral indexes, and continuum removal over water and cellulose absorption bands. The outputs of these transformations were used as inputs to a Random Forests classifier. Concurrent with image acquisition, field data (800-2000 points) were collected across the Delta for training and validation of the classification products. The field data were divided into test and training polygons. These polygons were overlaid on the transformed files and pixel data were extracted corresponding to the polygons. The training data were used to train the Random Forests classifier to identify 10 classes (water, submerged aquatic vegetation, emergent marsh, soil, non-photosynthetic vegetation, water hyacinth, water primrose, pennywort, shadow, riparian vegetation). The classifier was validated quantitatively using the test data at both pixel and polygon level using overall accuracy and kappa metrics. The classifier was then applied to all flightlines and class maps were produced. Mosaics of these class maps are published in this dataset.
DOI: 10.13020/nq7t-z663
title:  Data files of work on LaCoO3 using VASP 

description: Sample VASP input file used to study LaCoO3 (INCAR)
Band structures of LaCoO3 at each values of strain (used to determine carrier effective mass)
Wannier functions derived from e_g orbitals of LaCoO3 (used to determine splitting between dx2-y2 and dz2 orbitals)
description: INCAR file (VASP input file for LaCoO3)
Band structures (agr format)
Wannier functions (xsf format)
DOI: 10.13020/s690-4824
title: Evaluation of a broadband sound projected from the gates of a navigation lock in the Mississippi River shows it to be a weak deterrent for common carp and unable to block passage

description: There is an urgent need to block the passage of carp and other invasive fishes through
navigational locks in large rivers. Although the broadband sound of an outboard motor
has been shown to strongly repel three species of carp in laboratory flumes and to a
lesser extent inside of a lock chamber, it has not yet been tested to see if it can stop
carp from entering a lock. To test this possibility, we attached speakers to lock gates
and played the sound of an outboard motor while measuring its efficacy by tracking
free-ranging transplanted tagged common carp in its vicinity. Eight groups of 20 carp
were tested while the sound system was turned on and off for 2 week periods. When
the sound system was on, these carp spent approximately one-third less time in
front of the gates than when it was off which when modeled by GLMM was shown
to no greater than the effects of river discharge or temperature. Further, there was
no indication that this sound blocked carp from entering and presumably passing
through the lock. However, the number of times that tagged carp entered the lock
was low even when the sound was off. A number of factors may have contributed
to the limited efficacy of this deterrent system including the sound itself.
description: See Readme files.
DOI: 10.13020/p3xp-5x36
title: Pollination of a bee dependent forb in restored prairie: No evidence of pollen limitation in landscapes dominated by row crop agriculture

description: This data set was generated by an experiment wherein we examined how the amount of agriculture surrounding restored tallgrass prairies affects pollination within restorations by deploying sentinel arrays of a native bee-pollinated forb to 8 sites occurring along an agricultural land-use gradient in western Minnesota, USA. We conducted a pollen limitation experiment on our arrays to measure the effect of the landscape surrounding a restoration on pollination, hypothesizing that sites surrounded by more corn and soy, the dominant driver of habitat loss and fragmentation in this system, would experience decreased pollination. We also hand net bees at these sites to test whether agriculture limits bee abundance in these restorations. Very few studies examine both pollen limitation and pollinator abundance in restorations at a landscape scale. Our data set consists of seed set data for individual plants used in our arrays, restoration site information and the proportion agriculture surrounding each restoration, and bee abundance data for each site.
description: two csvs, one with seed set data and the other with bee abundance data, and one R script.